Class: Queries::Otu::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, 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,
  :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, #descriptor_query, #extract_query, #image_query, #loan_query, #object_global_id, #observation_query, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #taxon_name_query

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, #attribute_exact_facet, #deep_permit, included_annotator_facets, inverted_subqueries, #model_id_facet, #object_global_id_facet, params, #permitted_params, #project_id_facet, #set_nested_queries, #shared_and_clauses, #subquery_vector

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.



176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
 
# File 'lib/queries/otu/filter.rb', line 176

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)
  @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_notes_params(params)
  set_citations_params(params)
  set_depiction_params(params)
  set_data_attributes_params(params)
  set_tags_params(params)
end

Instance Attribute Details

#ancestrify ⇒ Object

!! 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



48
49
50
 
# File 'lib/queries/otu/filter.rb', line 48

def ancestrify
  @ancestrify
end

#asserted_distributions ⇒ True, ...

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



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

def asserted_distributions
  @asserted_distributions
end

#biological_association_id ⇒ Object

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



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

def biological_association_id
  @biological_association_id
end

#biological_associations ⇒ True, ...

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



164
165
166
 
# File 'lib/queries/otu/filter.rb', line 164

def biological_associations
  @biological_associations
end

#collecting_event_id ⇒ Object

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



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

def collecting_event_id
  @collecting_event_id
end

#collection_objects ⇒ True, ...

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



158
159
160
 
# File 'lib/queries/otu/filter.rb', line 158

def collection_objects
  @collection_objects
end

#contents ⇒ True, ...

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

Returns:

  • (True, False, nil) —

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



152
153
154
 
# File 'lib/queries/otu/filter.rb', line 152

def contents
  @contents
end

#coordinatify ⇒ Object

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



56
57
58
 
# File 'lib/queries/otu/filter.rb', line 56

def coordinatify
  @coordinatify
end

#descendants ⇒ Object

Returns Boolean.

Returns:

  • Boolean



84
85
86
 
# File 'lib/queries/otu/filter.rb', line 84

def descendants
  @descendants
end

#descriptor_id ⇒ Array

Parameters:

  • descriptor_id (String, Array)

Returns:

  • (Array) 


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

def descriptor_id
  @descriptor_id
end

#geo_json ⇒ Hash?

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

Returns:

  • (Hash, nil) —

    in geo_json format (no Feature …) ?!



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

def geo_json
  @geo_json
end

#geographic_area_id ⇒ Array

Parameters:

  • geographic_area_id (String, Array)

Returns:

  • (Array) 


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

def geographic_area_id
  @geographic_area_id
end

#geographic_area_mode ⇒ Boolean?

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)



130
131
132
 
# File 'lib/queries/otu/filter.rb', line 130

def geographic_area_mode
  @geographic_area_mode
end

#historical_determinations ⇒ Boolean?

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) 


102
103
104
 
# File 'lib/queries/otu/filter.rb', line 102

def historical_determinations
  @historical_determinations
end

#name ⇒ Object

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

Parameters:

  • name (String, Array)

Returns:

  • Array literal match against one or more Otu#name



61
62
63
 
# File 'lib/queries/otu/filter.rb', line 61

def name
  @name
end

#name_exact ⇒ Object

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

Returns:

  • Boolean if true then match on ‘name` exactly



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

def name_exact
  @name_exact
end

#observations ⇒ True, ...

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



170
171
172
 
# File 'lib/queries/otu/filter.rb', line 170

def observations
  @observations
end

#otu_id ⇒ Object

Returns Array one or more Otu ids.

Parameters:

  • otu_id (Integer, Array)

Returns:

  • Array one or more Otu ids



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

def otu_id
  @otu_id
end

#radius ⇒ Object

Integer in Meters

!! defaults to 100m



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

def radius
  @radius
end

#taxon_name ⇒ True, ...

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



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

def taxon_name
  @taxon_name
end

#taxon_name_id ⇒ Object

Returns Array one or more Otu taxon_name_id.

Parameters:

  • taxon_name_id (Integer, Array)

Returns:

  • Array one or more Otu taxon_name_id



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

def taxon_name_id
  @taxon_name_id
end

#with_name ⇒ Object

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

Returns:

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



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

def with_name
  @with_name
end

#wkt ⇒ Object

Parameters:

  • wkt (String) —

    A Spatial area in WKT format



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

def wkt
  @wkt
end

Instance Method Details

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

Returns:

  • (ActiveRecord::Relation) 


649
650
651
652
653
654
655
 
# File 'lib/queries/otu/filter.rb', line 649

def all(nil_empty = false)
  q = super
  q = coordinatify_result(q) if coordinatify
  q = ancestrify_result(q) if ancestrify

  q
end

#ancestrify_result(q) ⇒ Object

Goal is to get

* all OTUs and their coordinates via nomenclature



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
 
# File 'lib/queries/otu/filter.rb', line 586

def ancestrify_result(q)
  ancestrify_taxon_name_ids = q.all.pluck(:taxon_name_id)

  if ancestrify_taxon_name_ids.any?
    r = ::Queries::TaxonName::Filter.new(
      taxon_name_id: ancestrify_taxon_name_ids,
      ancestrify: true,
      project_id:
    )

    s = 'WITH tn_otu_anc AS (' + r.all.to_sql + ') ' +
      ::Otu
      .joins('JOIN tn_otu_anc AS tn_otu_anc1 on tn_otu_anc1.id = otus.taxon_name_id')
      .to_sql

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

  c = if a
        c = coordinatify_result(a)
      else
        q
      end
  c
end

#and_clauses ⇒ Object 



612
613
614
615
616
617
 
# File 'lib/queries/otu/filter.rb', line 612

def and_clauses
  [
    name_facet,
    taxon_name_facet,
  ]
end

#asserted_distribution_query_facet ⇒ Object 



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

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_facet ⇒ Object 



291
292
293
294
295
296
297
298
 
# File 'lib/queries/otu/filter.rb', line 291

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

#biological_association_id_facet ⇒ Object 



378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
 
# File 'lib/queries/otu/filter.rb', line 378

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_facet ⇒ Object 



455
456
457
458
459
460
461
462
463
464
465
466
467
468
 
# File 'lib/queries/otu/filter.rb', line 455

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_facet ⇒ Object

UNION, NOT EXISTS example



319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
 
# File 'lib/queries/otu/filter.rb', line 319

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_table ⇒ Object 



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

def biological_associations_table
  ::BiologicalAssociation.arel_table
end

#collecting_event_id_facet ⇒ Object 



367
368
369
370
371
372
373
374
375
376
 
# File 'lib/queries/otu/filter.rb', line 367

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 })
  elsif historical_determinations
    ::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: }).where.not(taxon_determinations: { position: 1 })
  else
    ::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: })
  end
end

#collecting_event_query_facet ⇒ Object 



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

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_facet ⇒ Object 



470
471
472
473
474
475
476
477
478
479
 
# File 'lib/queries/otu/filter.rb', line 470

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_facet ⇒ Object 



338
339
340
341
342
343
344
345
 
# File 'lib/queries/otu/filter.rb', line 338

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

#content_query_facet ⇒ Object 



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

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_facet ⇒ Object 



309
310
311
312
313
314
315
316
 
# File 'lib/queries/otu/filter.rb', line 309

def contents_facet
  return nil if contents.nil?
  if contents
    ::Otu.joins(:contents)
  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.



558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
 
# File 'lib/queries/otu/filter.rb', line 558

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])
end

#descriptor_id_facet ⇒ Object 



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

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_facet ⇒ Object 



514
515
516
517
518
519
520
521
522
523
 
# File 'lib/queries/otu/filter.rb', line 514

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

#extract_query_facet ⇒ Object 



492
493
494
495
496
497
498
499
500
501
 
# File 'lib/queries/otu/filter.rb', line 492

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

#from_wkt(wkt_shape) ⇒ Object 



269
270
271
272
273
274
275
276
277
 
# File 'lib/queries/otu/filter.rb', line 269

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
end

#geo_json_facet ⇒ Object 



279
280
281
282
283
284
285
286
287
288
289
 
# File 'lib/queries/otu/filter.rb', line 279

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_facet ⇒ Object 



399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
 
# File 'lib/queries/otu/filter.rb', line 399

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_facet ⇒ Object 



525
526
527
528
529
530
531
532
533
534
535
536
537
538
 
# File 'lib/queries/otu/filter.rb', line 525

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_clauses ⇒ Object 



619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
 
# File 'lib/queries/otu/filter.rb', line 619

def merge_clauses
  [
    asserted_distribution_query_facet,
    asserted_distributions_facet,
    biological_association_query_facet,
    collecting_event_query_facet,
    collection_object_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,
    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_facet ⇒ Object 



242
243
244
245
246
247
248
249
 
# File 'lib/queries/otu/filter.rb', line 242

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_facet ⇒ Object 



540
541
542
543
544
545
546
547
548
549
 
# File 'lib/queries/otu/filter.rb', line 540

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_facet ⇒ Object 



357
358
359
360
361
362
363
364
365
 
# File 'lib/queries/otu/filter.rb', line 357

def observations_facet
  return nil if observations.nil?

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

#taxon_name_facet ⇒ Object 



347
348
349
350
351
352
353
354
355
 
# File 'lib/queries/otu/filter.rb', line 347

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_facet ⇒ Object 



251
252
253
254
255
256
257
258
259
260
261
262
 
# File 'lib/queries/otu/filter.rb', line 251

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)
  else
    ::Otu.where(taxon_name_id:)
  end
end

#taxon_name_query_facet ⇒ Object 



503
504
505
506
507
508
509
510
511
512
 
# File 'lib/queries/otu/filter.rb', line 503

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_facet ⇒ Object 



300
301
302
303
304
305
306
307
 
# File 'lib/queries/otu/filter.rb', line 300

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_facet ⇒ Object 



264
265
266
267
 
# File 'lib/queries/otu/filter.rb', line 264

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