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,
  :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, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #taxon_name_query, #venn, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_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



293
294
295
296
297
298
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
# File 'lib/queries/taxon_name/filter.rb', line 293

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)
  @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

#ancestorsObject

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 :(



70
71
72
# File 'lib/queries/taxon_name/filter.rb', line 70

def ancestors
  @ancestors
end

#ancestrifyObject

!! 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



76
77
78
# File 'lib/queries/taxon_name/filter.rb', line 76

def ancestrify
  @ancestrify
end

#authorObject

Parameters:

  • author (String)

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



118
119
120
# File 'lib/queries/taxon_name/filter.rb', line 118

def author
  @author
end

#author_exactObject

Returns Boolean.

Returns:

  • Boolean



121
122
123
# File 'lib/queries/taxon_name/filter.rb', line 121

def author_exact
  @author_exact
end

#authorsObject

‘true’ or ‘false’

on initialize

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

Parameters:

  • authors (Boolean, nil)


230
231
232
# File 'lib/queries/taxon_name/filter.rb', line 230

def authors
  @authors
end

#collecting_event_idObject

Returns Array.

Parameters:

  • collecting_event_id (String, Array)

Returns:

  • Array



106
107
108
# File 'lib/queries/taxon_name/filter.rb', line 106

def collecting_event_id
  @collecting_event_id
end

#collection_object_idObject

Returns Array.

Parameters:

  • collection_object_id (String, Array)

Returns:

  • Array



85
86
87
# File 'lib/queries/taxon_name/filter.rb', line 85

def collection_object_id
  @collection_object_id
end

#combination_taxon_name_idArray

Returns taxon_name_ids for which all Combinations will be returned.

Returns:

  • (Array)

    taxon_name_ids for which all Combinations will be returned



280
281
282
# File 'lib/queries/taxon_name/filter.rb', line 280

def combination_taxon_name_id
  @combination_taxon_name_id
end

#combinationifyObject

!! 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



98
99
100
# File 'lib/queries/taxon_name/filter.rb', line 98

def combinationify
  @combinationify
end

#combinationsObject

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



92
93
94
# File 'lib/queries/taxon_name/filter.rb', line 92

def combinations
  @combinations
end

#descendantsBoolean

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?



174
175
176
# File 'lib/queries/taxon_name/filter.rb', line 174

def descendants
  @descendants
end

#descendants_max_depthInteger?

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)


181
182
183
# File 'lib/queries/taxon_name/filter.rb', line 181

def descendants_max_depth
  @descendants_max_depth
end

#epithet_onlyObject

Parameters:

  • epithet_only (Boolean)

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



81
82
83
# File 'lib/queries/taxon_name/filter.rb', line 81

def epithet_only
  @epithet_only
end

#etymologyObject

‘true’ or ‘false’

on initialize

whether the name has etymology

Parameters:

  • etymology (Boolean, nil)


225
226
227
# File 'lib/queries/taxon_name/filter.rb', line 225

def etymology
  @etymology
end

#geo_jsonObject

Returns the value of attribute geo_json.



289
290
291
# File 'lib/queries/taxon_name/filter.rb', line 289

def geo_json
  @geo_json
end

#leavesBoolean?

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



258
259
260
# File 'lib/queries/taxon_name/filter.rb', line 258

def leaves
  @leaves
end

#nameArray

Returns Matches against cached. See also name_exact.

Parameters:

  • name (String, Array)

Returns:

  • (Array)

    Matches against cached. See also name_exact.



111
112
113
# File 'lib/queries/taxon_name/filter.rb', line 111

def name
  @name
end

#name_exactObject

Returns Boolean.

Returns:

  • Boolean



114
115
116
# File 'lib/queries/taxon_name/filter.rb', line 114

def name_exact
  @name_exact
end

#nomenclature_codeString?

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

Returns:

  • (String, nil)

    accessor for attr :nomenclature_code, wrap with needed wildcards



251
252
253
# File 'lib/queries/taxon_name/filter.rb', line 251

def nomenclature_code
  @nomenclature_code
end

#nomenclature_dateObject

Returns Boolean with/out cached nomenclature date set.

Parameters:

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

Returns:

  • Boolean with/out cached nomenclature date set



131
132
133
# File 'lib/queries/taxon_name/filter.rb', line 131

def nomenclature_date
  @nomenclature_date
end

#nomenclature_groupString?

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

Returns:

  • (String, nil)

    accessor for attr :nomenclature_group, wrap with needed wildcards



247
248
249
# File 'lib/queries/taxon_name/filter.rb', line 247

def nomenclature_group
  @nomenclature_group
end

#not_specifiedObject

Returns the value of attribute not_specified.



242
243
244
# File 'lib/queries/taxon_name/filter.rb', line 242

def not_specified
  @not_specified
end

#original_combinationBoolean?

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



210
211
212
# File 'lib/queries/taxon_name/filter.rb', line 210

def original_combination
  @original_combination
end

#otu_idArray?

Returns one or more OTU ids.

Parameters:

  • otu_id (Array, nil)

Returns:

  • (Array, nil)

    one or more OTU ids



215
216
217
# File 'lib/queries/taxon_name/filter.rb', line 215

def otu_id
  @otu_id
end

#otusObject

‘true’ or ‘false’

on initialize

whether the name has an Otu

Parameters:

  • otus (Boolean, nil)


220
221
222
# File 'lib/queries/taxon_name/filter.rb', line 220

def otus
  @otus
end

#parent_idObject

Return the taxon names with this/these parent_ids

Returns:

  • Return the taxon names with this/these parent_ids



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

def parent_id
  @parent_id
end

#rankArray

Returns:

  • (Array)


287
288
289
# File 'lib/queries/taxon_name/filter.rb', line 287

def rank
  @rank
end

#sortString?

Parameters:

  • sort (String, nil)

    one of :classification, :alphabetical

Returns:

  • (String, nil)


276
277
278
# File 'lib/queries/taxon_name/filter.rb', line 276

def sort
  @sort
end

#synonymifyObject

!! 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



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

def synonymify
  @synonymify
end

#taxon_name_author_idArray

Returns:

  • (Array)


265
266
267
# File 'lib/queries/taxon_name/filter.rb', line 265

def taxon_name_author_id
  @taxon_name_author_id
end

#taxon_name_author_id_orBoolean

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)


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

def taxon_name_author_id_or
  @taxon_name_author_id_or
end

#taxon_name_classificationObject

Parameters:

  • taxon_name_classification (Array)

    Class names of TaxonNameClassification, as strings.



203
204
205
# File 'lib/queries/taxon_name/filter.rb', line 203

def taxon_name_classification
  @taxon_name_classification
end

#taxon_name_idObject

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

Returns:

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



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

def taxon_name_id
  @taxon_name_id
end

#taxon_name_relationshipObject

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’ } … {}


195
196
197
# File 'lib/queries/taxon_name/filter.rb', line 195

def taxon_name_relationship
  @taxon_name_relationship
end

#taxon_name_relationship_typeObject

Parameters:

  • taxon_name_relationship (Array)

    All names involved in any of these relationship



199
200
201
# File 'lib/queries/taxon_name/filter.rb', line 199

def taxon_name_relationship_type
  @taxon_name_relationship_type
end

#taxon_name_typeString?

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

Returns:

  • (String, nil)

    &taxon_name_type=<Protonym|Combination|Hybrid>



262
263
264
# File 'lib/queries/taxon_name/filter.rb', line 262

def taxon_name_type
  @taxon_name_type
end

#type_metadataObject

‘true’ or ‘false’

on initialize

whether the name has TypeMaterial


235
236
237
# File 'lib/queries/taxon_name/filter.rb', line 235

def 
  @type_metadata
end

#validifyObject

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

Returns:

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



153
154
155
# File 'lib/queries/taxon_name/filter.rb', line 153

def validify
  @validify
end

#validityObject

‘true’ or ‘false’

on initialize

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


146
147
148
# File 'lib/queries/taxon_name/filter.rb', line 146

def validity
  @validity
end

#yearObject

Matches against cached_author_year.

Parameters:

  • year (String)

    “yyyy”



126
127
128
# File 'lib/queries/taxon_name/filter.rb', line 126

def year
  @year
end

#year_endObject

Matches against cached_nomenclature_date

Parameters:

  • year_end (String)

    “yyyy”



141
142
143
# File 'lib/queries/taxon_name/filter.rb', line 141

def year_end
  @year_end
end

#year_startObject

Matches against cached_nomenclature_date

Parameters:

  • year_start (String)

    “yyyy”



136
137
138
# File 'lib/queries/taxon_name/filter.rb', line 136

def year_start
  @year_start
end

Instance Method Details

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

Returns:

  • (ActiveRecord::Relation)


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

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_facetObject

A merge facet.

Returns:

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



498
499
500
501
502
503
504
505
506
507
508
# File 'lib/queries/taxon_name/filter.rb', line 498

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



885
886
887
888
889
890
891
892
893
894
895
# File 'lib/queries/taxon_name/filter.rb', line 885

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_clausesActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation)


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

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

#asserted_distribution_query_facetObject



746
747
748
749
750
751
752
753
754
755
# File 'lib/queries/taxon_name/filter.rb', line 746

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_facetObject



675
676
677
678
679
680
681
682
# File 'lib/queries/taxon_name/filter.rb', line 675

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_facetObject

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

Returns:

  • Scope



528
529
530
531
532
533
# File 'lib/queries/taxon_name/filter.rb', line 528

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_facetObject



779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
# File 'lib/queries/taxon_name/filter.rb', line 779

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_facetObject



718
719
720
721
722
723
# File 'lib/queries/taxon_name/filter.rb', line 718

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_facetObject



768
769
770
771
772
773
774
775
776
777
# File 'lib/queries/taxon_name/filter.rb', line 768

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_facetObject



510
511
512
513
# File 'lib/queries/taxon_name/filter.rb', line 510

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_facetObject



757
758
759
760
761
762
763
764
765
766
# File 'lib/queries/taxon_name/filter.rb', line 757

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_facetObject



707
708
709
710
711
712
713
714
715
716
# File 'lib/queries/taxon_name/filter.rb', line 707

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



873
874
875
876
877
878
879
880
881
882
883
# File 'lib/queries/taxon_name/filter.rb', line 873

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_facetObject



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

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

#descendant_facetObject

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



468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
# File 'lib/queries/taxon_name/filter.rb', line 468

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_facetObject



424
425
426
427
428
429
430
431
432
433
# File 'lib/queries/taxon_name/filter.rb', line 424

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_facetObject

Returns Scope.

Returns:

  • Scope



550
551
552
553
# File 'lib/queries/taxon_name/filter.rb', line 550

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

#merge_clausesObject



812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
# File 'lib/queries/taxon_name/filter.rb', line 812

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,
    ,
    with_etymology_facet,
    year_range_facet,
  ]

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

  clauses.compact
end

#model_id_facetObject

Overrides base class



848
849
850
851
# File 'lib/queries/taxon_name/filter.rb', line 848

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

#name_facetObject



652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
# File 'lib/queries/taxon_name/filter.rb', line 652

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_facetObject



457
458
459
460
461
462
463
464
# File 'lib/queries/taxon_name/filter.rb', line 457

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_facetObject



435
436
437
438
439
440
441
442
443
444
445
446
# File 'lib/queries/taxon_name/filter.rb', line 435

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



897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
# File 'lib/queries/taxon_name/filter.rb', line 897

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_facetObject



448
449
450
451
452
453
454
455
# File 'lib/queries/taxon_name/filter.rb', line 448

def original_combination_facet
  return nil if original_combination.nil?
  if original_combination
    ::Protonym.joins(:original_combination_relationships)
  else
    ::Protonym.where.missing(:original_combination_relationships)
  end
end

#otu_id_facetObject



515
516
517
518
# File 'lib/queries/taxon_name/filter.rb', line 515

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

#otu_query_facetObject



735
736
737
738
739
740
741
742
743
744
# File 'lib/queries/taxon_name/filter.rb', line 735

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_facetObject

Returns Scope.

Returns:

  • Scope



621
622
623
624
625
# File 'lib/queries/taxon_name/filter.rb', line 621

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_facetObject



670
671
672
673
# File 'lib/queries/taxon_name/filter.rb', line 670

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

#rank_facetArel::Nodes::Grouping?

Returns:

  • (Arel::Nodes::Grouping, nil)


634
635
636
637
638
639
# File 'lib/queries/taxon_name/filter.rb', line 634

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



862
863
864
865
866
867
868
869
870
871
# File 'lib/queries/taxon_name/filter.rb', line 862

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_facetObject



585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
# File 'lib/queries/taxon_name/filter.rb', line 585

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_facetObject

Returns Scope.

Returns:

  • Scope



573
574
575
576
577
578
579
580
581
582
583
# File 'lib/queries/taxon_name/filter.rb', line 573

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!



557
558
559
560
561
562
563
564
565
566
567
568
569
570
# File 'lib/queries/taxon_name/filter.rb', line 557

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_facetObject

Returns Scope.

Returns:

  • Scope



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

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_facetObject



647
648
649
650
# File 'lib/queries/taxon_name/filter.rb', line 647

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

#type_metadata_facetObject

Returns Scope.

Returns:

  • Scope



614
615
616
617
618
# File 'lib/queries/taxon_name/filter.rb', line 614

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

#validify_result(q) ⇒ Object



853
854
855
856
857
858
859
860
# File 'lib/queries/taxon_name/filter.rb', line 853

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_facetObject



698
699
700
701
702
703
704
705
# File 'lib/queries/taxon_name/filter.rb', line 698

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

#with_etymology_facetObject

Returns Scope.

Returns:

  • Scope



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

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

#with_nomenclature_codeArel::Nodes::Grouping?

Returns:

  • (Arel::Nodes::Grouping, nil)


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

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

#with_nomenclature_groupArel::Nodes::Grouping?

Returns:

  • (Arel::Nodes::Grouping, nil)


628
629
630
631
# File 'lib/queries/taxon_name/filter.rb', line 628

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

#year_facetObject



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

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_facetObject



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

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