Class: Queries::TaxonName::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, 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, #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, #deep_permit, included_annotator_facets, instatiated_base_filter, inverted_subqueries, #object_global_id_facet, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #shared_and_clauses, #subquery_vector, #venn_query

Methods inherited from Query

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

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.

Parameters:

  • params (Params) —

    as permitted via controller



299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
 
# File 'lib/queries/taxon_name/filter.rb', line 299

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_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 :(



71
72
73
 
# File 'lib/queries/taxon_name/filter.rb', line 71

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



77
78
79
 
# File 'lib/queries/taxon_name/filter.rb', line 77

def ancestrify
  @ancestrify
end

#author ⇒ Object

Parameters:

  • author (String) —

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



119
120
121
 
# File 'lib/queries/taxon_name/filter.rb', line 119

def author
  @author
end

#author_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



122
123
124
 
# File 'lib/queries/taxon_name/filter.rb', line 122

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) 


236
237
238
 
# File 'lib/queries/taxon_name/filter.rb', line 236

def authors
  @authors
end

#collecting_event_id ⇒ Object

Returns Array.

Parameters:

  • collecting_event_id (String, Array)

Returns:

  • Array



107
108
109
 
# File 'lib/queries/taxon_name/filter.rb', line 107

def collecting_event_id
  @collecting_event_id
end

#collection_object_id ⇒ Object

Returns Array.

Parameters:

  • collection_object_id (String, Array)

Returns:

  • Array



86
87
88
 
# File 'lib/queries/taxon_name/filter.rb', line 86

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



286
287
288
 
# File 'lib/queries/taxon_name/filter.rb', line 286

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



99
100
101
 
# File 'lib/queries/taxon_name/filter.rb', line 99

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



93
94
95
 
# File 'lib/queries/taxon_name/filter.rb', line 93

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?



180
181
182
 
# File 'lib/queries/taxon_name/filter.rb', line 180

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) 


187
188
189
 
# File 'lib/queries/taxon_name/filter.rb', line 187

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



82
83
84
 
# File 'lib/queries/taxon_name/filter.rb', line 82

def epithet_only
  @epithet_only
end

#etymology ⇒ Object

‘true’ or ‘false’

on initialize

whether the name has etymology

Parameters:

  • etymology (Boolean, nil) 


231
232
233
 
# File 'lib/queries/taxon_name/filter.rb', line 231

def etymology
  @etymology
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



295
296
297
 
# File 'lib/queries/taxon_name/filter.rb', line 295

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



264
265
266
 
# File 'lib/queries/taxon_name/filter.rb', line 264

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.



112
113
114
 
# File 'lib/queries/taxon_name/filter.rb', line 112

def name
  @name
end

#name_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



115
116
117
 
# File 'lib/queries/taxon_name/filter.rb', line 115

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



257
258
259
 
# File 'lib/queries/taxon_name/filter.rb', line 257

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



132
133
134
 
# File 'lib/queries/taxon_name/filter.rb', line 132

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



253
254
255
 
# File 'lib/queries/taxon_name/filter.rb', line 253

def nomenclature_group
  @nomenclature_group
end

#not_specified ⇒ Object

Returns the value of attribute not_specified.



248
249
250
 
# File 'lib/queries/taxon_name/filter.rb', line 248

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



216
217
218
 
# File 'lib/queries/taxon_name/filter.rb', line 216

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



221
222
223
 
# File 'lib/queries/taxon_name/filter.rb', line 221

def otu_id
  @otu_id
end

#otus ⇒ Object

‘true’ or ‘false’

on initialize

whether the name has an Otu

Parameters:

  • otus (Boolean, nil) 


226
227
228
 
# File 'lib/queries/taxon_name/filter.rb', line 226

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



171
172
173
 
# File 'lib/queries/taxon_name/filter.rb', line 171

def parent_id
  @parent_id
end

#rank ⇒ Array

Returns:

  • (Array) 


293
294
295
 
# File 'lib/queries/taxon_name/filter.rb', line 293

def rank
  @rank
end

#sort ⇒ String?

Parameters:

  • sort (String, nil) —

    one of :classification, :alphabetical

Returns:

  • (String, nil) 


282
283
284
 
# File 'lib/queries/taxon_name/filter.rb', line 282

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



193
194
195
 
# File 'lib/queries/taxon_name/filter.rb', line 193

def synonymify
  @synonymify
end

#taxon_name_author_id ⇒ Array

Returns:

  • (Array) 


271
272
273
 
# File 'lib/queries/taxon_name/filter.rb', line 271

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) 


277
278
279
 
# File 'lib/queries/taxon_name/filter.rb', line 277

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.



209
210
211
 
# File 'lib/queries/taxon_name/filter.rb', line 209

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



165
166
167
 
# File 'lib/queries/taxon_name/filter.rb', line 165

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’ } … {} 


201
202
203
 
# File 'lib/queries/taxon_name/filter.rb', line 201

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



205
206
207
 
# File 'lib/queries/taxon_name/filter.rb', line 205

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>



268
269
270
 
# File 'lib/queries/taxon_name/filter.rb', line 268

def taxon_name_type
  @taxon_name_type
end

#type_metadata ⇒ Object

‘true’ or ‘false’

on initialize

whether the name has TypeMaterial



241
242
243
 
# File 'lib/queries/taxon_name/filter.rb', line 241

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



154
155
156
 
# File 'lib/queries/taxon_name/filter.rb', line 154

def validify
  @validify
end

#validity ⇒ Object

‘true’ or ‘false’

on initialize

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



147
148
149
 
# File 'lib/queries/taxon_name/filter.rb', line 147

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



159
160
161
 
# File 'lib/queries/taxon_name/filter.rb', line 159

def verbatim_name
  @verbatim_name
end

#year ⇒ Object

Matches against cached_author_year.

Parameters:

  • year (String) —

    “yyyy”



127
128
129
 
# File 'lib/queries/taxon_name/filter.rb', line 127

def year
  @year
end

#year_end ⇒ Object

Matches against cached_nomenclature_date

Parameters:

  • year_end (String) —

    “yyyy”



142
143
144
 
# File 'lib/queries/taxon_name/filter.rb', line 142

def year_end
  @year_end
end

#year_start ⇒ Object

Matches against cached_nomenclature_date

Parameters:

  • year_start (String) —

    “yyyy”



137
138
139
 
# File 'lib/queries/taxon_name/filter.rb', line 137

def year_start
  @year_start
end

Instance Method Details

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

Returns:

  • (ActiveRecord::Relation) 


934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
 
# File 'lib/queries/taxon_name/filter.rb', line 934

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



506
507
508
509
510
511
512
513
514
515
516
 
# File 'lib/queries/taxon_name/filter.rb', line 506

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 



903
904
905
906
907
908
909
910
911
912
913
 
# File 'lib/queries/taxon_name/filter.rb', line 903

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) 


814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
 
# File 'lib/queries/taxon_name/filter.rb', line 814

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 



763
764
765
766
767
768
769
770
771
772
 
# File 'lib/queries/taxon_name/filter.rb', line 763

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 



683
684
685
686
687
688
689
690
 
# File 'lib/queries/taxon_name/filter.rb', line 683

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



536
537
538
539
540
541
 
# File 'lib/queries/taxon_name/filter.rb', line 536

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 



796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
 
# File 'lib/queries/taxon_name/filter.rb', line 796

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 



735
736
737
738
739
740
 
# File 'lib/queries/taxon_name/filter.rb', line 735

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 



785
786
787
788
789
790
791
792
793
794
 
# File 'lib/queries/taxon_name/filter.rb', line 785

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 



518
519
520
521
 
# File 'lib/queries/taxon_name/filter.rb', line 518

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 



774
775
776
777
778
779
780
781
782
783
 
# File 'lib/queries/taxon_name/filter.rb', line 774

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 



724
725
726
727
728
729
730
731
732
733
 
# File 'lib/queries/taxon_name/filter.rb', line 724

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 



891
892
893
894
895
896
897
898
899
900
901
 
# File 'lib/queries/taxon_name/filter.rb', line 891

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 



742
743
744
745
746
747
748
749
750
 
# File 'lib/queries/taxon_name/filter.rb', line 742

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



476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
 
# File 'lib/queries/taxon_name/filter.rb', line 476

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 



432
433
434
435
436
437
438
439
440
441
 
# File 'lib/queries/taxon_name/filter.rb', line 432

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



558
559
560
561
 
# File 'lib/queries/taxon_name/filter.rb', line 558

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

#merge_clauses ⇒ Object 



830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
 
# File 'lib/queries/taxon_name/filter.rb', line 830

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



866
867
868
869
 
# File 'lib/queries/taxon_name/filter.rb', line 866

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

#name_facet ⇒ Object 



660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
 
# File 'lib/queries/taxon_name/filter.rb', line 660

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 



465
466
467
468
469
470
471
472
 
# File 'lib/queries/taxon_name/filter.rb', line 465

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 



443
444
445
446
447
448
449
450
451
452
453
454
 
# File 'lib/queries/taxon_name/filter.rb', line 443

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 



915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
 
# File 'lib/queries/taxon_name/filter.rb', line 915

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 



456
457
458
459
460
461
462
463
 
# File 'lib/queries/taxon_name/filter.rb', line 456

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 



523
524
525
526
 
# File 'lib/queries/taxon_name/filter.rb', line 523

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

#otu_query_facet ⇒ Object 



752
753
754
755
756
757
758
759
760
761
 
# File 'lib/queries/taxon_name/filter.rb', line 752

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



629
630
631
632
633
 
# File 'lib/queries/taxon_name/filter.rb', line 629

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 



678
679
680
681
 
# File 'lib/queries/taxon_name/filter.rb', line 678

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) 


642
643
644
645
646
647
 
# File 'lib/queries/taxon_name/filter.rb', line 642

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 



880
881
882
883
884
885
886
887
888
889
 
# File 'lib/queries/taxon_name/filter.rb', line 880

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 



593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
 
# File 'lib/queries/taxon_name/filter.rb', line 593

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



581
582
583
584
585
586
587
588
589
590
591
 
# File 'lib/queries/taxon_name/filter.rb', line 581

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!



565
566
567
568
569
570
571
572
573
574
575
576
577
578
 
# File 'lib/queries/taxon_name/filter.rb', line 565

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



552
553
554
555
 
# File 'lib/queries/taxon_name/filter.rb', line 552

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 



655
656
657
658
 
# File 'lib/queries/taxon_name/filter.rb', line 655

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



622
623
624
625
626
 
# File 'lib/queries/taxon_name/filter.rb', line 622

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 



871
872
873
874
875
876
877
878
 
# File 'lib/queries/taxon_name/filter.rb', line 871

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 



706
707
708
709
710
711
712
713
 
# File 'lib/queries/taxon_name/filter.rb', line 706

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 



715
716
717
718
719
720
721
722
 
# File 'lib/queries/taxon_name/filter.rb', line 715

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



544
545
546
547
548
549
 
# File 'lib/queries/taxon_name/filter.rb', line 544

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) 


650
651
652
653
 
# File 'lib/queries/taxon_name/filter.rb', line 650

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) 


636
637
638
639
 
# File 'lib/queries/taxon_name/filter.rb', line 636

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

#year_facet ⇒ Object 



692
693
694
695
696
697
698
 
# File 'lib/queries/taxon_name/filter.rb', line 692

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 



700
701
702
703
704
 
# File 'lib/queries/taxon_name/filter.rb', line 700

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