Class: Queries::Otu::Filter

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

Constant Summary collapse

PARAMS =
[
  :ancestrify,
  :asserted_distributions,
  :biological_association_id,
  :biological_associations,
  :collecting_event_id,
  :collection_objects,
  :common_names,
  :contents,
  :coordinatify,
  :descendants,
  :descriptor_id,
  :geo_json,
  :geographic_area_id,
  :geographic_area_mode,
  :name,
  :name_exact,
  :observations,
  :otu_id,
  :radius,
  :taxon_name,
  :taxon_name_id,
  :with_name,
  :wkt,

  collecting_event_id: [],
  descriptor_id: [],
  geographic_area_id: [],
  name: [],
  otu_id: [],
  taxon_name_id: [],
].freeze

Constants inherited from Query::Filter

Query::Filter::FILTER_QUERIES, Query::Filter::SUBQUERIES

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #controlled_vocabulary_term_query, #data_attribute_query, #depiction_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #order_by, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #recent_target, #sound_query, #taxon_name_query, #venn, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_param, #integer_param

Methods inherited from Query::Filter

#all_and_clauses, #all_merge_clauses, #annotator_and_clauses, #annotator_merge_clauses, annotator_params, api_except_params, api_excluded_params, #apply_venn, #attribute_exact_facet, base_filter, base_query_name, base_query_to_h, #deep_permit, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #model_id_facet, #object_global_id_facet, #only_project?, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #shared_and_clauses, #subquery_vector, #target_and_clauses, #venn_query

Methods inherited from Query

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

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.



186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
# File 'lib/queries/otu/filter.rb', line 186

def initialize(query_params)
  super

  @ancestrify = boolean_param(params, :ancestrify)
  @asserted_distributions = boolean_param(params, :asserted_distributions)
  @biological_association_id = params[:biological_association_id]
  @biological_associations = boolean_param(params, :biological_associations)
  @collecting_event_id = params[:collecting_event_id]
  @collection_objects = boolean_param(params, :collection_objects)
  @common_names = boolean_param(params, :common_names)
  @contents = boolean_param(params, :contents)
  @coordinatify = boolean_param(params, :coordinatify)
  @descendants = boolean_param(params, :descendants)
  @descriptor_id = params[:descriptor_id]
  @geo_json = params[:geo_json]
  @geographic_area_id = params[:geographic_area_id]
  @geographic_area_mode = boolean_param(params, :geographic_area_mode)
  @historical_determinations = boolean_param(params, :historical_determinations)
  @name = params[:name]
  @name_exact = boolean_param(params, :name_exact)
  @observations = boolean_param(params, :observations)
  @otu_id = params[:otu_id]
  @radius = params[:radius].presence || 100.0
  @taxon_name = boolean_param(params, :taxon_name)
  @taxon_name_id = params[:taxon_name_id]
  @with_name = boolean_param(params, :with_name)
  @wkt = params[:wkt]

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

Instance Attribute Details

#ancestrifyObject

!! This param is not like the others. !! See parallel in TaxonName filter ‘ancestrify’.

Returns:

  • Boolean if true then, additionally, all coordinate otus for all inferred ancestors are included the param adds to the result by going “up” (to root) then “out”



52
53
54
# File 'lib/queries/otu/filter.rb', line 52

def ancestrify
  @ancestrify
end

#asserted_distributionsTrue, ...

Returns true - Otu has AssertedDistribution false - Otu without AssertedDistribution nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has AssertedDistribution false - Otu without AssertedDistribution nil - not applied



150
151
152
# File 'lib/queries/otu/filter.rb', line 150

def asserted_distributions
  @asserted_distributions
end

#biological_association_idObject

Finds all OTUs that are the current determination of a CollectionObject that is in the BiologicalAssociation or are part of the Biological association itself. Altered by historical_determinations.

Parameters:

  • biological_association_id (Integer, Array)

Returns:

  • Array one or more biological_association_id



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

def biological_association_id
  @biological_association_id
end

#biological_associationsTrue, ...

Returns true - Otu has BiologicalAssocation (subject or object) false - Otu without BiologicalAssociation nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has BiologicalAssocation (subject or object) false - Otu without BiologicalAssociation nil - not applied



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

def biological_associations
  @biological_associations
end

#collecting_event_idObject

Finds all OTUs that are the current determination of a CollectionObject that was collecting in these Collecting events. Altered by historical_determinations.

Parameters:

  • collecting_event_id (Integer, Array)

Returns:

  • Array one or more collecting_event_id



97
98
99
# File 'lib/queries/otu/filter.rb', line 97

def collecting_event_id
  @collecting_event_id
end

#collection_objectsTrue, ...

Returns true - Otu has CollectionObjects false - Otu without CollectionObjects nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has CollectionObjects false - Otu without CollectionObjects nil - not applied



168
169
170
# File 'lib/queries/otu/filter.rb', line 168

def collection_objects
  @collection_objects
end

#common_namesTrue, ...

Returns true - Otu has common names false - Otu without common names nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has common names false - Otu without common names nil - not applied



156
157
158
# File 'lib/queries/otu/filter.rb', line 156

def common_names
  @common_names
end

#contentsTrue, ...

Returns true - Otu has Content false - Otu without Content nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has Content false - Otu without Content nil - not applied



162
163
164
# File 'lib/queries/otu/filter.rb', line 162

def contents
  @contents
end

#coordinatifyObject

See ‘coordinatify_result` for more.

!! This param is not like the others. !! See parallel in TaxonName filter ‘validify’.

Returns:

  • Boolean if true then, additionally, all coordinate otus for the result are included



60
61
62
# File 'lib/queries/otu/filter.rb', line 60

def coordinatify
  @coordinatify
end

#descendantsObject

Returns Boolean.

Returns:

  • Boolean



88
89
90
# File 'lib/queries/otu/filter.rb', line 88

def descendants
  @descendants
end

#descriptor_idArray

Parameters:

  • descriptor_id (String, Array)

Returns:

  • (Array)


144
145
146
# File 'lib/queries/otu/filter.rb', line 144

def descriptor_id
  @descriptor_id
end

#geo_jsonHash?

Returns in geo_json format (no Feature …) ?!.

Returns:

  • (Hash, nil)

    in geo_json format (no Feature …) ?!



123
124
125
# File 'lib/queries/otu/filter.rb', line 123

def geo_json
  @geo_json
end

#geographic_area_idArray

Parameters:

  • geographic_area_id (String, Array)

Returns:

  • (Array)


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

def geographic_area_id
  @geographic_area_id
end

#geographic_area_modeBoolean?

Returns How to treat GeographicAreas

nil - non-spatial match by only those records matching the geographic_area_id exactly
true - spatial match
false - non-spatial match (exact and descendants).

Returns:

  • (Boolean, nil)

    How to treat GeographicAreas

    nil - non-spatial match by only those records matching the geographic_area_id exactly
    true - spatial match
    false - non-spatial match (exact and descendants)
    


134
135
136
# File 'lib/queries/otu/filter.rb', line 134

def geographic_area_mode
  @geographic_area_mode
end

#historical_determinationsBoolean?

Where applicable:

true - include only historical determinations (ignores only determinations)
false - include both current and historical
nil - include only current determinations

Impacts all TaxonDetermination referencing queries

Parameters:

  • historical_determinations (Boolean)

Returns:

  • (Boolean, nil)


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

def historical_determinations
  @historical_determinations
end

#nameObject

Returns Array literal match against one or more Otu#name.

Parameters:

  • name (String, Array)

Returns:

  • Array literal match against one or more Otu#name



65
66
67
# File 'lib/queries/otu/filter.rb', line 65

def name
  @name
end

#name_exactObject

Returns Boolean if true then match on ‘name` exactly.

Returns:

  • Boolean if true then match on ‘name` exactly



69
70
71
# File 'lib/queries/otu/filter.rb', line 69

def name_exact
  @name_exact
end

#observationsTrue, ...

Returns true - Otu has observations false - Otu without observations nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has observations false - Otu without observations nil - not applied



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

def observations
  @observations
end

#otu_idObject

Returns Array one or more Otu ids.

Parameters:

  • otu_id (Integer, Array)

Returns:

  • Array one or more Otu ids



80
81
82
# File 'lib/queries/otu/filter.rb', line 80

def otu_id
  @otu_id
end

#radiusObject

Integer in Meters

!! defaults to 100m


184
185
186
# File 'lib/queries/otu/filter.rb', line 184

def radius
  @radius
end

#taxon_nameTrue, ...

Returns true - Otu has taxon name false - Otu without taxon name nil - not applied.

Returns:

  • (True, False, nil)

    true - Otu has taxon name false - Otu without taxon name nil - not applied



140
141
142
# File 'lib/queries/otu/filter.rb', line 140

def taxon_name
  @taxon_name
end

#taxon_name_idObject

Returns Array one or more Otu taxon_name_id.

Parameters:

  • taxon_name_id (Integer, Array)

Returns:

  • Array one or more Otu taxon_name_id



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

def taxon_name_id
  @taxon_name_id
end

#with_nameObject

Returns Boolean true - has name false - has no name nil - both.

Returns:

  • Boolean true - has name false - has no name nil - both



75
76
77
# File 'lib/queries/otu/filter.rb', line 75

def with_name
  @with_name
end

#wktObject

Parameters:

  • wkt (String)

    A Spatial area in WKT format



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

def wkt
  @wkt
end

Instance Method Details

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

Returns:

  • (ActiveRecord::Relation)


696
697
698
699
700
701
702
703
704
# File 'lib/queries/otu/filter.rb', line 696

def all(nil_empty = false)
  q = super

  # Order matters, coordinatify should be last as its "out"
  q = ancestrify_result(q) if ancestrify
  q = coordinatify_result(q) if coordinatify

  q
end

#ancestrify_result(q) ⇒ Object



642
643
644
645
646
647
648
649
650
651
652
653
654
# File 'lib/queries/otu/filter.rb', line 642

def ancestrify_result(q)
  a = q

  s = 'WITH otu_base AS (' + a.all.to_sql + ') ' +
    ::Otu
    .joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = otus.taxon_name_id')
    .joins('JOIN otu_base as otu_base1 on otu_base1.taxon_name_id = tnh.descendant_id')
    .to_sql

  b = ::Otu.from('(' + s + ') as otus')

  referenced_klass_union([a, b])
end

#and_clausesObject



656
657
658
659
660
661
# File 'lib/queries/otu/filter.rb', line 656

def and_clauses
  [
    name_facet,
    taxon_name_facet,
  ]
end

#asserted_distribution_query_facetObject



458
459
460
461
462
463
464
465
466
# File 'lib/queries/otu/filter.rb', line 458

def asserted_distribution_query_facet
  return nil if asserted_distribution_query.nil?
  s = 'WITH query_ad_otus AS (' + asserted_distribution_query.all.to_sql + ') ' +
    ::Otu
    .joins('JOIN query_ad_otus as query_ad_otus1 on otus.id = query_ad_otus1.otu_id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#asserted_distributions_facetObject



304
305
306
307
308
309
310
311
# File 'lib/queries/otu/filter.rb', line 304

def asserted_distributions_facet
  return nil if asserted_distributions.nil?
  if asserted_distributions
    ::Otu.joins(:asserted_distributions).distinct
  else
    ::Otu.where.missing(:asserted_distributions)
  end
end

#biological_association_id_facetObject



401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
# File 'lib/queries/otu/filter.rb', line 401

def biological_association_id_facet
  return nil if biological_association_id.empty?

  q1 = ::Otu.joins(:biological_associations).where(biological_associations: { id: biological_association_id, biological_association_subject_type: 'Otu' })
  q2 = ::Otu.joins(:related_biological_associations).where(related_biological_associations: { id: biological_association_id, biological_association_object_type: 'Otu' })
  q3 = ::Otu.joins(collection_objects: [:biological_associations]).where(biological_associations: { id: biological_association_id, biological_association_subject_type: 'CollectionObject' })
  q4 = ::Otu.joins(collection_objects: [:related_biological_associations]).where(related_biological_associations: { id: biological_association_id, biological_association_object_type: 'CollectionObject' })

  if historical_determinations.nil?
    q3 = q3.where(taxon_determinations: { position: 1 })
    q4 = q4.where(taxon_determinations: { position: 1 })
  elsif historical_determinations
    q3 = q3.where.not(taxon_determinations: { position: 1 })
    q4 = q4.where.not(taxon_determinations: { position: 1 })
  end

  query = referenced_klass_union([q1, q2, q3, q4])

  ::Otu.from("(#{query.to_sql}) as otus").distinct
end

#biological_association_query_facetObject



478
479
480
481
482
483
484
485
486
487
488
489
490
491
# File 'lib/queries/otu/filter.rb', line 478

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

  a = ::Otu
    .joins("JOIN query_ba_otu as query_ba_otu1 on otus.id = query_ba_otu1.biological_association_subject_id AND query_ba_otu1.biological_association_subject_type = 'Otu'")

  b = ::Otu
    .joins("JOIN query_ba_otu as query_ba_otu2 on otus.id = query_ba_otu2.biological_association_object_id AND query_ba_otu2.biological_association_object_type = 'Otu'")

  s << referenced_klass_union([a, b]).to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#biological_associations_facetObject

UNION, NOT EXISTS example



342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
# File 'lib/queries/otu/filter.rb', line 342

def biological_associations_facet
  return nil if biological_associations.nil?

  a = ::Otu.joins(:biological_associations)
  b = ::Otu.joins(:related_biological_associations)

  c = ::Otu.from("((#{a.to_sql}) UNION (#{b.to_sql})) as otus")

  if biological_associations
    ::Otu.from("((#{a.to_sql}) UNION (#{b.to_sql})) as otus")
  else
    ::Otu.where('NOT EXISTS (' + ::Otu.select('1').from( # not exists ( a select(1) from <opposite query>  )
                                                        ::Otu.from(
                                                          "((#{a.to_sql}) UNION (#{b.to_sql})) as ba_otus_join"
                                                        ).where('otus.id = ba_otus_join.id')
                                                       ).to_sql + ')')  # where includes in/out link
  end
end

#biological_associations_tableObject



223
224
225
# File 'lib/queries/otu/filter.rb', line 223

def biological_associations_table
  ::BiologicalAssociation.arel_table
end

#collecting_event_id_facetObject



390
391
392
393
394
395
396
397
398
399
# File 'lib/queries/otu/filter.rb', line 390

def collecting_event_id_facet
  return nil if collecting_event_id.empty?
  if historical_determinations.nil?
    ::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: }, taxon_determinations: { position: 1 }).distinct
  elsif historical_determinations
    ::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: }).where.not(taxon_determinations: { position: 1 }).distinct
  else
    ::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: })
  end
end

#collecting_event_query_facetObject



515
516
517
518
519
520
521
522
523
524
# File 'lib/queries/otu/filter.rb', line 515

def collecting_event_query_facet
  return nil if collecting_event_query.nil?
  s = 'WITH query_ce_otus AS (' + collecting_event_query.all.to_sql + ') ' +
    ::Otu
    .joins(:collecting_events)
    .joins('JOIN query_ce_otus as query_ce_otus1 on collecting_events.id = query_ce_otus1.id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#collection_object_query_facetObject



493
494
495
496
497
498
499
500
501
502
# File 'lib/queries/otu/filter.rb', line 493

def collection_object_query_facet
  return nil if collection_object_query.nil?
  s = 'WITH query_co_otus AS (' + collection_object_query.all.to_sql + ') ' +
    ::Otu
    .joins(:collection_objects)
    .joins('JOIN query_co_otus as query_co_otus1 on collection_objects.id = query_co_otus1.id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#collection_objects_facetObject



361
362
363
364
365
366
367
368
# File 'lib/queries/otu/filter.rb', line 361

def collection_objects_facet
  return nil if collection_objects.nil?
  if collection_objects
    ::Otu.joins(:collection_objects).distinct
  else
    ::Otu.where.missing(:collection_objects)
  end
end

#common_names_facetObject



331
332
333
334
335
336
337
338
339
# File 'lib/queries/otu/filter.rb', line 331

def common_names_facet
  return nil if @common_names.nil?

  if @common_names
    ::Otu.joins(:common_names).distinct
  else
    ::Otu.where.missing(:common_names)
  end
end

#content_query_facetObject



468
469
470
471
472
473
474
475
476
# File 'lib/queries/otu/filter.rb', line 468

def content_query_facet
  return nil if content_query.nil?
  s = 'WITH query_con_otus AS (' + content_query.all.to_sql + ') ' +
    ::Otu
    .joins('JOIN query_con_otus as query_con_otus1 on otus.id = query_con_otus1.otu_id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#contents_facetObject



322
323
324
325
326
327
328
329
# File 'lib/queries/otu/filter.rb', line 322

def contents_facet
  return nil if contents.nil?
  if contents
    ::Otu.joins(:contents).distinct
  else
    ::Otu.where.missing(:contents)
  end
end

#coordinatify_result(q) ⇒ Object

Expands result of OTU filter query in 2 ways:

1 - to include all valid OTUs by (proxy of TaxonName) if OTU is by proxy invalid
2 - to include all invalid OTUS (by proxy of TaxonName) if OTU is by proxy valid

In essence this creates full sets of TaxonConcepts from partial results. The result can be used to, for example, get a comprehensive list of Sources for the concept, or a comprehensive historical list of Specimens, etc.



616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
# File 'lib/queries/otu/filter.rb', line 616

def coordinatify_result(q)

  i = q.joins(:taxon_name).where('taxon_names.id != taxon_names.cached_valid_taxon_name_id').where(project_id:)
  v = q.joins(:taxon_name).where('taxon_names.id = taxon_names.cached_valid_taxon_name_id').where(project_id:)

  # Find valid for invalid
  s = 'WITH invalid_otu_result AS (' + i.to_sql + ') ' +
    ::Otu
    .joins('JOIN taxon_names tn1 on otus.taxon_name_id = tn1.cached_valid_taxon_name_id')
    .joins('JOIN invalid_otu_result AS invalid_otu_result1 ON invalid_otu_result1.taxon_name_id = tn1.id') # invalid otus matching valid names
    .to_sql

  a = ::Otu.from('(' + s + ') as otus')

  # Find invalid for valid
  t = 'WITH valid_otu_result AS (' + v.to_sql + ') ' +
    ::Otu
    .joins('JOIN taxon_names tn2 on otus.taxon_name_id = tn2.id')
    .joins('JOIN valid_otu_result AS valid_otu_result1 ON valid_otu_result1.taxon_name_id = tn2.cached_valid_taxon_name_id') # valid otus matching invalid names
    .to_sql

  b = ::Otu.from('(' + t + ') as otus')

  referenced_klass_union([a, b, q]).distinct # Unions shouldn't need distinct
end

#descriptor_id_facetObject



449
450
451
452
453
454
455
456
# File 'lib/queries/otu/filter.rb', line 449

def descriptor_id_facet
  return nil if descriptor_id.empty?

  q1 = ::Otu.joins(:descriptors).where(descriptors: { id: descriptor_id })
  q2 = ::Otu.joins(collection_objects: [:descriptors]).where(descriptors: { id: descriptor_id })

  referenced_klass_union([q1, q2]).distinct
end

#descriptor_query_facetObject



548
549
550
551
552
553
554
555
556
557
# File 'lib/queries/otu/filter.rb', line 548

def descriptor_query_facet
  return nil if descriptor_query.nil?
  s = 'WITH query_de_otus AS (' + descriptor_query.all.to_sql + ') ' +
    ::Otu
    .joins(:observations)
    .joins('JOIN query_de_otus as query_de_otus1 on observations.descriptor_id = query_de_otus1.id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#dwc_occurrence_query_facetObject

!! This is a soft-link (i.e. no otu_id FK directly), so latency between indexing has a very small proability !! of impacting the results.



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

def dwc_occurrence_query_facet
  return nil if dwc_occurrence_query.nil?

  a = dwc_occurrence_query.all.object_join('CollectionObject').select(dwc_occurrences: [:dwc_occurrence_object_id])
  b = dwc_occurrence_query.all.object_join('AssertedDistribution').select(dwc_occurrences: [:dwc_occurrence_object_id])
  c = dwc_occurrence_query.all.object_join('FieldOccurrence').select(dwc_occurrences: [:dwc_occurrence_object_id])

  d = ::Otu.with(co: a)
        .joins(:taxon_determinations).where(taxon_determinations: {position: 1})
        .joins('JOIN co on co.dwc_occurrence_object_id = taxon_determinations.taxon_determination_object_id')

  e = ::Otu.with(ad: b)
        .joins(:asserted_distributions)
        .joins('JOIN ad on ad.dwc_occurrence_object_id = asserted_distributions.id')

  f = ::Otu.with(fo: c)
        .joins(:taxon_determinations).where(taxon_determinations: {position: 1})
        .joins('JOIN fo on fo.dwc_occurrence_object_id = taxon_determinations.taxon_determination_object_id')

  ::Queries.union(::Otu, [d,e,f])
end

#extract_query_facetObject



526
527
528
529
530
531
532
533
534
535
# File 'lib/queries/otu/filter.rb', line 526

def extract_query_facet
  return nil if extract_query.nil?
  s = 'WITH query_ex_otus AS (' + extract_query.all.to_sql + ') ' +
    ::Otu
    .joins(:origin_relationships)
    .joins("JOIN query_ex_otus as query_ex_otus1 on origin_relationships.new_object_id = query_ex_otus1.id and origin_relationships.new_object_type = 'Extract'")
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#field_occurrence_query_facetObject



504
505
506
507
508
509
510
511
512
513
# File 'lib/queries/otu/filter.rb', line 504

def field_occurrence_query_facet
  return nil if field_occurrence_query.nil?
  s = 'WITH query_fo_otus AS (' + field_occurrence_query.all.to_sql + ') ' +
    ::Otu
    .joins(:field_occurrences)
    .joins('JOIN query_fo_otus as query_fo_otus1 on field_occurrences.id = query_fo_otus1.id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#from_wkt(wkt_shape) ⇒ Object



282
283
284
285
286
287
288
289
290
# File 'lib/queries/otu/filter.rb', line 282

def from_wkt(wkt_shape)
  c = ::Queries::CollectingEvent::Filter.new(wkt: wkt_shape, project_id:)
  a = ::Queries::AssertedDistribution::Filter.new(wkt: wkt_shape, project_id:)

  q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
  q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)

  referenced_klass_union([q1, q2]).distinct # Not needed, union should be distinct
end

#geo_json_facetObject



292
293
294
295
296
297
298
299
300
301
302
# File 'lib/queries/otu/filter.rb', line 292

def geo_json_facet
  return nil if geo_json.blank?

  c = ::Queries::CollectingEvent::Filter.new(geo_json:, project_id:, radius:)
  a = ::Queries::AssertedDistribution::Filter.new(geo_json:, project_id:, radius:)

  q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
  q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)

  referenced_klass_union([q1, q2]).distinct
end

#geographic_area_id_facetObject



422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
# File 'lib/queries/otu/filter.rb', line 422

def geographic_area_id_facet
  return nil if geographic_area_id.empty?
  a = nil

  case geographic_area_mode
  when nil, true # exact and spatial start the same
    a = ::GeographicArea.where(id: geographic_area_id)
  when false # descendants
    a = ::GeographicArea.descendants_of_any(geographic_area_id)
  end

  b = nil # from AssertedDistributions
  c = nil # from CollectionObjects

  case geographic_area_mode
  when nil, false # exact, descendants
    b = ::Otu.joins(:asserted_distributions).where(asserted_distributions: { geographic_area: a })
    c = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: { geographic_area: a })
  when true # spatial
    i = ::GeographicItem.joins(:geographic_areas).where(geographic_areas: a) # .unscope
    wkt_shape = ::GeographicItem.st_union(i).to_a.first['collection'].to_s # todo, check
    return from_wkt(wkt_shape)
  end

  referenced_klass_union([b, c])
end

#loan_query_facetObject



559
560
561
562
563
564
565
566
567
568
569
570
571
572
# File 'lib/queries/otu/filter.rb', line 559

def loan_query_facet
  return nil if loan_query.nil?
  s = 'WITH query_loan_otus AS (' + loan_query.all.to_sql + ') '

  a = ::Otu.joins(:loan_items)
    .joins('JOIN query_loan_otus as query_loan_otus1 on loan_items.loan_id = query_loan_otus1.id')

  b = ::Otu.joins(collection_objects: [:loan_items])
    .joins('JOIN query_loan_otus as query_loan_otus1 on loan_items.loan_id = query_loan_otus1.id')

  s << referenced_klass_union([a, b]).to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#merge_clausesObject



663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
# File 'lib/queries/otu/filter.rb', line 663

def merge_clauses
  [
    asserted_distribution_query_facet,
    asserted_distributions_facet,
    biological_association_query_facet,
    collecting_event_query_facet,
    collection_object_query_facet,
    dwc_occurrence_query_facet,
    field_occurrence_query_facet,
    content_query_facet,
    descriptor_query_facet,
    extract_query_facet,
    loan_query_facet,
    observation_query_facet,
    taxon_name_query_facet,

    biological_association_id_facet,
    biological_associations_facet,
    collecting_event_id_facet,
    collection_objects_facet,
    common_names_facet,
    contents_facet,
    descriptor_id_facet,
    geo_json_facet,
    geographic_area_id_facet,
    observations_facet,
    taxon_name_id_facet,
    with_name_facet,
    wkt_facet,
  ].compact
end

#name_facetObject



255
256
257
258
259
260
261
262
# File 'lib/queries/otu/filter.rb', line 255

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

#observation_query_facetObject



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

def observation_query_facet
  return nil if observation_query.nil?
  s = 'WITH query_obs_otus AS (' + observation_query.all.to_sql + ') ' +
    ::Otu
    .joins(:observations)
    .joins('JOIN query_obs_otus as query_obs_otus1 on observations.id = query_obs_otus1.id')
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#observations_facetObject



380
381
382
383
384
385
386
387
388
# File 'lib/queries/otu/filter.rb', line 380

def observations_facet
  return nil if observations.nil?

  if observations
    ::Otu.joins(:observations).distinct
  else
    ::Otu.where.missing(:observations)
  end
end

#taxon_name_facetObject



370
371
372
373
374
375
376
377
378
# File 'lib/queries/otu/filter.rb', line 370

def taxon_name_facet
  return nil if taxon_name.nil?

  if taxon_name
    table[:taxon_name_id].not_eq(nil)
  else
    table[:taxon_name_id].eq(nil)
  end
end

#taxon_name_id_facetObject



264
265
266
267
268
269
270
271
272
273
274
275
# File 'lib/queries/otu/filter.rb', line 264

def taxon_name_id_facet
  return nil if taxon_name_id.empty?
  if descendants
    h = Arel::Table.new(:taxon_name_hierarchies)
    j = table.join(h, Arel::Nodes::InnerJoin).on(table[:taxon_name_id].eq(h[:descendant_id]))
    z = h[:ancestor_id].in(taxon_name_id)

    ::Otu.joins(j.join_sources).where(z).distinct # Maybe not needed
  else
    ::Otu.where(taxon_name_id:)
  end
end

#taxon_name_query_facetObject



537
538
539
540
541
542
543
544
545
546
# File 'lib/queries/otu/filter.rb', line 537

def taxon_name_query_facet
  return nil if taxon_name_query.nil?
  s = 'WITH query_taxon_names AS (' + taxon_name_query.all.to_sql + ') ' +
    ::Otu
    .joins('JOIN query_taxon_names as query_taxon_names1 on otus.taxon_name_id = query_taxon_names1.id')
    .where.not(taxon_name_id: nil) # .joins(:taxon_name)
    .to_sql

  ::Otu.from('(' + s + ') as otus').distinct
end

#with_name_facetObject



313
314
315
316
317
318
319
320
# File 'lib/queries/otu/filter.rb', line 313

def with_name_facet
  return nil if with_name.nil?
  if with_name
    ::Otu.where.not(name: nil)
  else
    ::Otu.where(name: nil)
  end
end

#wkt_facetObject



277
278
279
280
# File 'lib/queries/otu/filter.rb', line 277

def wkt_facet
  return nil if wkt.nil?
  from_wkt(wkt)
end