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,
  :cached,
  :collecting_event_id,
  :collection_object_id,
  :combinations,
  :combinationify,
  :descendants,
  :descendants_max_depth,
  :epithet_only,
  :etymology,
  :latinized,
  :leaves,
  :name,
  :name_exact,
  :nomenclature_code,
  :nomenclature_date,
  :nomenclature_group, # !! different than autocomplete
  :not_specified,
  :original_combination,
  :otu_id,
  :otus,
  :rank,
  :relation_to_relationship,
  :sort,
  :taxon_name_relationship_target,
  :synonymify,
  :taxon_name_author_id_or,
  :taxon_name_id,
  :taxon_name_type,
  :type_metadata,
  :validify,
  :validity,
  :verbatim_name,
  :year,
  :year_end,
  :year_start,

  cached: [],
  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_subject: [],
  taxon_name_relationship_type_object: [],
  taxon_name_relationship_type_either: [],
  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, #conveyance_query, #data_attribute_query, #depiction_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #order_by, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #recent_target, #roll_call, #sound_query, #taxon_name_query, #taxon_name_relationship_query, #venn, #venn_ignore_pagination, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_param, #integer_param

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

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #base_query, #build_terms, #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 346

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)
  @cached = params[:cached]
  @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]
  @latinized = boolean_param(params, :latinized)
  @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]
  @relation_to_relationship = params[:relation_to_relationship]
  @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_target = params[:taxon_name_relationship_target]
  @taxon_name_relationship_type_subject =
    params[:taxon_name_relationship_type_subject] || []
  @taxon_name_relationship_type_object =
    params[:taxon_name_relationship_type_object] || []
  @taxon_name_relationship_type_either =
    params[:taxon_name_relationship_type_either] || []
  @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 80

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 86

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 132

def author
  @author
end

#author_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



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# File 'lib/queries/taxon_name/filter.rb', line 135

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 263

def authors
  @authors
end

#cached ⇒ Array

Returns of TaxonNames matching cached exactly.

Parameters:

  • cached (String, Array)

Returns:

  • (Array) —

    of TaxonNames matching cached exactly



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

def cached
  @cached
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 116

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 95

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 322

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 108

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 102

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 193

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 200

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 91

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 258

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 331

def geo_json
  @geo_json
end

#latinized ⇒ Boolean?

Returns &latinized=<“true”|“false”> if ‘true’ then return only genus group names with gender and species

group names with part of speech

if ‘false’ then return only genus group names without gender and

species group names without part of speech

if nil, ignore.

Returns:

  • (Boolean, nil) —

    &latinized=<“true”|“false”> if ‘true’ then return only genus group names with gender and species

    group names with part of speech

    if ‘false’ then return only genus group names without gender and

    species group names without part of speech

    if nil, ignore



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

def latinized
  @latinized
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 291

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 121

def name
  @name
end

#name_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



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# File 'lib/queries/taxon_name/filter.rb', line 124

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 284

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 145

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 280

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 275

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 243

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 248

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 253

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 184

def parent_id
  @parent_id
end

#rank ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/taxon_name/filter.rb', line 329

def rank
  @rank
end

#relation_to_relationship ⇒ String?

Returns &relation_to_relationship=<subject|object|either> All names that are subject|object|either of any relationship.

Returns:

  • (String, nil) —

    &relation_to_relationship=<subject|object|either> All names that are subject|object|either of any relationship



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

def relation_to_relationship
  @relation_to_relationship
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 318

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 206

def synonymify
  @synonymify
end

#taxon_name_author_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/taxon_name/filter.rb', line 307

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 313

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 236

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 178

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 214

def taxon_name_relationship
  @taxon_name_relationship
end

#taxon_name_relationship_target ⇒ Boolean

Applies only to taxon_name_relationship_query_facet, is only present in queries sent from Filter TaxonNameRelationship.

Parameters:

  • taxon_name_relationship_target (Boolean)

Returns:

  • (Boolean) —

    • ‘subject’: only return subjects of relationships from taxon_name_relationship_query_facet

    • ‘object’: only return objects of relationships from taxon_name_relationship_query_facet

    • nil: return both subjects and objects



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

def taxon_name_relationship_target
  @taxon_name_relationship_target
end

#taxon_name_relationship_type_either ⇒ Object

Parameters:

  • taxon_name_relationship_type_either (Array) —

    All names involved in any of these relationships as either subject or object



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# File 'lib/queries/taxon_name/filter.rb', line 227

def taxon_name_relationship_type_either
  @taxon_name_relationship_type_either
end

#taxon_name_relationship_type_object ⇒ Object

Parameters:

  • taxon_name_relationship_type_object (Array) —

    All names involved in any of these relationships as object



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

def taxon_name_relationship_type_object
  @taxon_name_relationship_type_object
end

#taxon_name_relationship_type_subject ⇒ Object

Parameters:

  • taxon_name_relationship_type_subject (Array) —

    All names involved in any of these relationships as subject



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

def taxon_name_relationship_type_subject
  @taxon_name_relationship_type_subject
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 304

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 268

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 167

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 160

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 172

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 140

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 155

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 150

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 1103

def all(nil_empty = false)
  # Everything below subqueries on q in some way, so q can't have paging
  # enabled.
  paging_state = disable_paging
  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
  if sort
    q = order_clause(q)
    paging_state[:ordered] = true
  end

  q = self.class.set_paging(q, paging_state)

  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 563

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 1072

def ancestrify_result(q)
  s = ::TaxonName
     .with(tn_q4: q)
    .joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = taxon_names.id')
    .joins('JOIN tn_q4 ON tn_q4.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 979

def and_clauses
  [
    nomenclature_date_facet,
    author_facet,
    cached_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 902

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 822

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 593

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 935

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

#cached_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 812

def cached_facet
  return nil if cached.empty?
  table[:cached].in(cached)
end

#collecting_event_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 874

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 924

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 575

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 913

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 863

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 1060

def combinationify_result(q)
  s = ::TaxonName
    .with(tn_q3: q)
    .joins('JOIN tn_q3 ON tn_q3.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 881

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 533

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 489

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

#latinized_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 648

def latinized_facet
  return nil if latinized.nil?

  tnc = ::TaxonNameClassification.arel_table
  if latinized == true
    # Note the query here does not restrict to genus/species groups - a
    # genus whose rank is changed to subfamily can retain its gender,
    # e.g., and we want to include those here.
    ::TaxonName.where(
      ::TaxonNameClassification.where(
        tnc[:taxon_name_id].eq(table[:id]).and(
          tnc[:type].in(LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES)
        )
      ).arel.exists
    )
  else
    ::TaxonName
      .where(
        table[:rank_class].in(GENUS_AND_SPECIES_RANK_NAMES)
      )
      .where.not(
        ::TaxonNameClassification.where(
          tnc[:taxon_name_id].eq(table[:id]).and(
            tnc[:type].in(LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES)
          )
        ).arel.exists
      )
  end
end

#leaves_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 642

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 996

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

    ancestor_facet,
    authors_facet,
    collecting_event_id_facet,
    collection_object_id_facet,
    combination_taxon_name_id_facet,
    combinations_facet,
    descendant_facet,
    latinized_facet,
    leaves_facet,
    not_specified_facet,
    original_combination_facet,
    otu_id_facet,
    otus_facet,
    relation_to_relationship_facet,
    taxon_name_author_id_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 1035

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 794

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 522

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 500

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 1084

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 513

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 580

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 891

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 763

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 817

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 776

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

#relation_to_relationship_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 697

def relation_to_relationship_facet
  return nil if relation_to_relationship.nil?

  if relation_to_relationship == 'subject'
    ::TaxonName.with_taxon_name_relationships_as_subject.distinct
  elsif relation_to_relationship == 'object'
    ::TaxonName.with_taxon_name_relationships_as_object.distinct
  else
    # 3-4x more time-performant than using
    # :with_taxon_name_relationships.distinct
    ::TaxonName.joins('join taxon_name_relationships ON ' \
      'taxon_names.id = taxon_name_relationships.subject_taxon_name_id OR ' \
      'taxon_names.id = taxon_name_relationships.object_taxon_name_id'
    ).distinct
  end
end

#synonimify_result(q) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 1049

def synonimify_result(q)
  s = ::TaxonName
    .with(tn_q2: q)
    .joins('JOIN tn_q2 ON tn_q2.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 727

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 715

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 680

def taxon_name_relationship_facet(hsh)
  hsh = hsh.symbolize_keys
  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_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 952

def taxon_name_relationship_query_facet
  return nil if taxon_name_relationship_query.nil?

  a = nil
  b = nil
  if taxon_name_relationship_target == 'subject' ||
     taxon_name_relationship_target.nil?
    a = ::TaxonName
      .with(tnr_query: taxon_name_relationship_query.all)
      .joins(:taxon_name_relationships)
      .where('taxon_name_relationships.id IN (SELECT id FROM tnr_query)')
      .distinct
  end

  if taxon_name_relationship_target == 'object' ||
     taxon_name_relationship_target.nil?
    b = ::TaxonName
      .with(tnr_query: taxon_name_relationship_query.all)
      .joins(:related_taxon_name_relationships)
      .where('taxon_name_relationships.id IN (SELECT id FROM tnr_query)')
      .distinct
  end

  referenced_klass_union([a,b])
end

#taxon_name_relationship_type_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 609

def taxon_name_relationship_type_facet
  if taxon_name_relationship_type_subject.empty? &&
     taxon_name_relationship_type_object.empty? &&
     taxon_name_relationship_type_either.empty?
    return nil
  end

  s = nil
  o = nil
  e = nil

  if taxon_name_relationship_type_subject.present?
    s = ::TaxonName.as_subject_with_taxon_name_relationship(
      taxon_name_relationship_type_subject
    ).distinct
  end

  if taxon_name_relationship_type_object.present?
    o = ::TaxonName.as_object_with_taxon_name_relationship(
      taxon_name_relationship_type_object
    ).distinct
  end

  if taxon_name_relationship_type_either.present?
    e = ::TaxonName.with_taxon_name_relationship(
      taxon_name_relationship_type_either
    )
  end

  referenced_klass_union([s, o, e])
end

#taxon_name_type_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 789

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 756

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 1040

def validify_result(q)
  s = ::TaxonName
    .with(tn_q1: q)
    .joins('JOIN tn_q1 ON tn_q1.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 845

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 854

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 601

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 784

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 770

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 831

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 839

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