Class: Otu

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, MatrixHooks, Shared::BiologicalAssociations, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::Depictions, Shared::HasPapertrail, Shared::Identifiers, Shared::IsData, Shared::Loanable, Shared::MatrixHooks::Member, Shared::Notes, Shared::Observations, Shared::OriginRelationship, Shared::Tags, SoftValidation
Defined in:
app/models/otu.rb

Overview

An Otu (loosely, operational taxonomic unit) can be thought of as a unit of study. In most cases an otu is a taxon.

An Otu is defined by its underlying data and may be labeled with a name (TaxonName). Otus are used to represent rows in matrices, taxon pages, individuals or populations, or arbitrary clusters of organisms (e.g. 'unsorted specimens in this container'). Otus are a primary unit of work in TaxonWorks.

OTU is labeled with a name, either arbitrarily given or specifically linked to a taxon_name_id.

TODO Semantics vs. taxon_name_id

Defined Under Namespace

Modules: MatrixHooks Classes: Autocomplete, Filter

Constant Summary collapse

GRAPH_ENTRY_POINTS = 
[:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations]

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from MatrixHooks

#member_of_new_matrix_row_items, #member_of_old_matrix_row_items

Methods included from Shared::MatrixHooks::Member

#member_add_matrix_columns, #member_add_matrix_rows, #member_add_to_matrix_items, #member_of_new_matrix_column_items, #member_of_new_matrix_row_items, #member_of_old_matrix_column_items, #member_of_old_matrix_row_items, #member_remove_from_matrix_items, #member_remove_matrix_columns, #member_remove_matrix_rows, #member_syncronize_matrices, #member_update_matrix_items?

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Loanable

#has_been_loaned?, #is_loanable?, #loan_return_date, #on_loan?, #times_loaned

Methods included from Shared::Depictions

#has_depictions?, #image_array=, #reject_depictions, #reject_images

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from SoftValidation

#clear_soft_validations, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#name ⇒ String

A label for the OTU.

Returns:

  • (String) 


24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
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
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
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
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
 
# File 'app/models/otu.rb', line 24

class Otu < ApplicationRecord
  include Housekeeping
  include SoftValidation
  #include Shared::AlternateValues   # No alternate values on Name!!
  include Shared::Citations          # TODO: have to think hard about this vs. using Nico's framework
  include Shared::DataAttributes
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::Depictions
  include Shared::Loanable
  include Shared::Confidences
  include Shared::Observations
  include Shared::BiologicalAssociations
  include Shared::HasPapertrail
  include Shared::OriginRelationship

  include Shared::MatrixHooks::Member
  include Otu::MatrixHooks

  include Shared::IsData

  is_origin_for 'Sequence', 'Extract'

  GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations]

  belongs_to :taxon_name, inverse_of: :otus

  has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error

  has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error
  has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error

  has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change
  has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus

  has_many :extracts, through: :collection_objects, source: :extracts
  has_many :sequences, through: :extracts, source: :derived_sequences

  has_many :collecting_events, -> { distinct }, through: :collection_objects
  has_many :common_names, dependent: :destroy
  has_many :collection_profiles, dependent: :restrict_with_error  # @proceps dependent: what?
  has_many :contents, inverse_of: :otu, dependent: :destroy
  has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area
  has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area
  has_many :georeferences, through: :collecting_events

  has_many :content_topics, through: :contents, source: :topic

  has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu'
  has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all
  has_many :observation_matrices, through: :observation_matrix_rows

  has_many :observations, inverse_of: :otu, dependent: :restrict_with_error
  has_many :descriptors, through: :observations

  scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) }
  scope :with_name, -> (name) { where(name: name) }

  # @return Scope
  def self.alphabetically
    includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC')
  end

  # @param [Integer] otu_id
  # @param [String] rank_class
  # @return [Scope]
  #    Otu.joins(:taxon_name).where(taxon_name: q).to_sql
  def self.self_and_descendants_of(otu_id, rank_class = nil)
    if o = Otu.joins(:taxon_name).find(otu_id)
      if rank_class.nil?
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants)
      else
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class))
      end
    else # no taxon name just return self in scope
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #
  # All OTUs that are synonymous/same/matching target, for either
  #    historical and pragmatic (i.e. share the same `taxon_name_id`), or
  #    nomenclatural reasons (are synonyms of the taxon name). Includes self.
  #
  def self.coordinate_otus(otu_id)
    begin
      i = Otu.joins(:taxon_name).find(otu_id)
      j = i.taxon_name.cached_valid_taxon_name_id
      o = Otu.arel_table
      t = TaxonName.arel_table

      q = o.join(t, Arel::Nodes::InnerJoin).on(
        o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j))
      )

      Otu.joins(q.join_sources)
    rescue ActiveRecord::RecordNotFound
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #   if the Otu is a child, via synonymy or not, of the taxon name
  #   !! Invalid taxon_name_ids return nothing
  #   !! Taxon names with synonyms return the OTUs of their synonyms
  def self.descendant_of_taxon_name(taxon_name_id)
    o = Otu.arel_table
    t = TaxonName.arel_table
    h = TaxonNameHierarchy.arel_table

    q = o.join(t, Arel::Nodes::InnerJoin).on(
      o[:taxon_name_id].eq( t[:id]))
      .join(h, Arel::Nodes::InnerJoin).on(
        t[:cached_valid_taxon_name_id].eq(h[:descendant_id]))

    Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql)
  end

  def current_collection_objects
    collection_objects.where(taxon_determinations: {position: 1})
  end

  validate :check_required_fields

  soft_validate(:sv_taxon_name, set: :taxon_name)
  soft_validate(:sv_duplicate_otu, set: :duplicate_otu)

  accepts_nested_attributes_for :common_names, allow_destroy: true

  # @return [Otu#id, nil, false]
  #  nil - there is no OTU parent with a valid taxon name possible
  #  false - there is > 1 OTU parent with a valid taxon name possible
  #  id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name
  #
  #  Note this is used CoLDP export. Do not change without considerations there.
  def parent_otu_id
    return nil if taxon_name_id.nil?

    # TODO: Unify to a single query

    candidates = TaxonName.joins(:otus, :descendant_hierarchies)
      .that_is_valid
      .where.not(id: taxon_name_id)
      .where(taxon_name_hierarchies: {descendant_id: taxon_name_id})
      .order('taxon_name_hierarchies.generations')
      .limit(1)
      .pluck(:id)

    if candidates.size == 1
      otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load
      if otus.size == 1
        return otus.first.id
      elsif otus.count > 1
        return false
      else
      return nil
      end
    else
      return nil
    end
  end

  # @return [Array]
  #   all bilogical associations this Otu is part of
  def all_biological_associations
    # !! If self relationships are ever made possible this needs a DISTINCT clause
    BiologicalAssociation.find_by_sql(
      "SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_subject_id = #{self.id}
           AND biological_associations.biological_association_subject_type = 'Otu'
       UNION
       SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_object_id = #{self.id}
           AND biological_associations.biological_association_object_type = 'Otu' ")
  end

  # return [Scope] the Otus bound to that taxon name and its descendants
  def self.for_taxon_name(taxon_name)
    if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer)
      tn = TaxonName.find(taxon_name)
    else
      tn = taxon_name
    end
    Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id})
  end

  # TODO: This need to be renamed to reflect "simple" association
  def self.batch_preview(file: nil, ** args)
    # f     = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol)
    @otus = []
    File.open(file).each do |row|
      name = row.strip
      next if name.blank?
      @otus.push(Otu.new(name: row.strip))
    end
    @otus
  end

  def self.batch_create(otus: {}, ** args)
    new_otus = []
    begin
      Otu.transaction do
        otus.each_key do |k|
          o = Otu.new(otus[k])
          o.save!
          new_otus.push(o)
        end
      end
    rescue
      return false
    end
    new_otus
  end

  # @return [Boolean]
  #   whether or not this otu is coordinate (see coordinate_otus) with this otu
  def coordinate_with?(otu_id)
    Otu.coordinate_otus(otu_id).where(otus: {id: id}).any?
  end

  # Hernán - this is extremely hacky, I'd like to
  # map core keys to procs, use yield:, use cached values,
  # add logic for has_many handling (e.g. identifiers) etc.
  # ultmately, each key maps to a proc that returns a value
  #
  # deprecated for new approach in CollectionObject, AssertedDistribution
  def dwca_core
    core = Dwca::GbifProfile::CoreTaxon.new

    core.nomenclaturalCode        = (taxon_name.rank_class.nomenclatural_code.to_s.upcase)
    core.taxonomicStatus          = (taxon_name.unavailable_or_invalid? ? nil : 'accepted')
    core.nomenclaturalStatus      = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking
    core.scientificName           = taxon_name.cached
    core.scientificNameAuthorship = taxon_name.cached_author_year
    core.scientificNameID         = taxon_name.identifiers.first.identifier
    core.taxonRank                = taxon_name.rank
    core.namePublishedIn          = taxon_name.source.cached
    core
  end

  # TODO: Deprecate for helper method, HTML does not belong here
  def otu_name
    if !name.blank?
      name
    elsif !taxon_name_id.nil?
      taxon_name.cached_html_name_and_author_year
    else
      nil
    end
  end

  # TODO: move to helper method likely
  def distribution_geoJSON
    a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions)
    c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences)
    c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area)
    Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution)
  end

  # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        when 'Content'
          Content.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        else
          return Otu.none
        end

    p = Otu.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_object_type'].eq('Otu')
              )
          )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['otu_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')

    case used_on
        when 'BiologicalAssociation'
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_object_id'].eq(p['id'])
          ))
        else
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id'])))
        end

    Otu.joins(j).pluck(:id).uniq
  end

  # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination'
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

    if target && !r.empty?
      h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a +
          Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now)
              .order('updated_at DESC')
              .limit(3).to_a
              ).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
    else
      h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
    end

    h
  end

  protected

  def check_required_fields
    if taxon_name_id.blank? && name.blank?
      errors.add(:taxon_name_id, 'and/or name should be selected')
      errors.add(:name, 'and/or taxon name should be selected')
    end
  end

  def sv_taxon_name
    soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil?
  end

  def sv_duplicate_otu
    unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty?
      m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project"
      soft_validations.add(:taxon_name_id, m)
      soft_validations.add(:name, m )
    end
  end

end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
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
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
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
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
 
# File 'app/models/otu.rb', line 24

class Otu < ApplicationRecord
  include Housekeeping
  include SoftValidation
  #include Shared::AlternateValues   # No alternate values on Name!!
  include Shared::Citations          # TODO: have to think hard about this vs. using Nico's framework
  include Shared::DataAttributes
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::Depictions
  include Shared::Loanable
  include Shared::Confidences
  include Shared::Observations
  include Shared::BiologicalAssociations
  include Shared::HasPapertrail
  include Shared::OriginRelationship

  include Shared::MatrixHooks::Member
  include Otu::MatrixHooks

  include Shared::IsData

  is_origin_for 'Sequence', 'Extract'

  GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations]

  belongs_to :taxon_name, inverse_of: :otus

  has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error

  has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error
  has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error

  has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change
  has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus

  has_many :extracts, through: :collection_objects, source: :extracts
  has_many :sequences, through: :extracts, source: :derived_sequences

  has_many :collecting_events, -> { distinct }, through: :collection_objects
  has_many :common_names, dependent: :destroy
  has_many :collection_profiles, dependent: :restrict_with_error  # @proceps dependent: what?
  has_many :contents, inverse_of: :otu, dependent: :destroy
  has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area
  has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area
  has_many :georeferences, through: :collecting_events

  has_many :content_topics, through: :contents, source: :topic

  has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu'
  has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all
  has_many :observation_matrices, through: :observation_matrix_rows

  has_many :observations, inverse_of: :otu, dependent: :restrict_with_error
  has_many :descriptors, through: :observations

  scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) }
  scope :with_name, -> (name) { where(name: name) }

  # @return Scope
  def self.alphabetically
    includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC')
  end

  # @param [Integer] otu_id
  # @param [String] rank_class
  # @return [Scope]
  #    Otu.joins(:taxon_name).where(taxon_name: q).to_sql
  def self.self_and_descendants_of(otu_id, rank_class = nil)
    if o = Otu.joins(:taxon_name).find(otu_id)
      if rank_class.nil?
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants)
      else
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class))
      end
    else # no taxon name just return self in scope
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #
  # All OTUs that are synonymous/same/matching target, for either
  #    historical and pragmatic (i.e. share the same `taxon_name_id`), or
  #    nomenclatural reasons (are synonyms of the taxon name). Includes self.
  #
  def self.coordinate_otus(otu_id)
    begin
      i = Otu.joins(:taxon_name).find(otu_id)
      j = i.taxon_name.cached_valid_taxon_name_id
      o = Otu.arel_table
      t = TaxonName.arel_table

      q = o.join(t, Arel::Nodes::InnerJoin).on(
        o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j))
      )

      Otu.joins(q.join_sources)
    rescue ActiveRecord::RecordNotFound
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #   if the Otu is a child, via synonymy or not, of the taxon name
  #   !! Invalid taxon_name_ids return nothing
  #   !! Taxon names with synonyms return the OTUs of their synonyms
  def self.descendant_of_taxon_name(taxon_name_id)
    o = Otu.arel_table
    t = TaxonName.arel_table
    h = TaxonNameHierarchy.arel_table

    q = o.join(t, Arel::Nodes::InnerJoin).on(
      o[:taxon_name_id].eq( t[:id]))
      .join(h, Arel::Nodes::InnerJoin).on(
        t[:cached_valid_taxon_name_id].eq(h[:descendant_id]))

    Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql)
  end

  def current_collection_objects
    collection_objects.where(taxon_determinations: {position: 1})
  end

  validate :check_required_fields

  soft_validate(:sv_taxon_name, set: :taxon_name)
  soft_validate(:sv_duplicate_otu, set: :duplicate_otu)

  accepts_nested_attributes_for :common_names, allow_destroy: true

  # @return [Otu#id, nil, false]
  #  nil - there is no OTU parent with a valid taxon name possible
  #  false - there is > 1 OTU parent with a valid taxon name possible
  #  id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name
  #
  #  Note this is used CoLDP export. Do not change without considerations there.
  def parent_otu_id
    return nil if taxon_name_id.nil?

    # TODO: Unify to a single query

    candidates = TaxonName.joins(:otus, :descendant_hierarchies)
      .that_is_valid
      .where.not(id: taxon_name_id)
      .where(taxon_name_hierarchies: {descendant_id: taxon_name_id})
      .order('taxon_name_hierarchies.generations')
      .limit(1)
      .pluck(:id)

    if candidates.size == 1
      otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load
      if otus.size == 1
        return otus.first.id
      elsif otus.count > 1
        return false
      else
      return nil
      end
    else
      return nil
    end
  end

  # @return [Array]
  #   all bilogical associations this Otu is part of
  def all_biological_associations
    # !! If self relationships are ever made possible this needs a DISTINCT clause
    BiologicalAssociation.find_by_sql(
      "SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_subject_id = #{self.id}
           AND biological_associations.biological_association_subject_type = 'Otu'
       UNION
       SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_object_id = #{self.id}
           AND biological_associations.biological_association_object_type = 'Otu' ")
  end

  # return [Scope] the Otus bound to that taxon name and its descendants
  def self.for_taxon_name(taxon_name)
    if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer)
      tn = TaxonName.find(taxon_name)
    else
      tn = taxon_name
    end
    Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id})
  end

  # TODO: This need to be renamed to reflect "simple" association
  def self.batch_preview(file: nil, ** args)
    # f     = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol)
    @otus = []
    File.open(file).each do |row|
      name = row.strip
      next if name.blank?
      @otus.push(Otu.new(name: row.strip))
    end
    @otus
  end

  def self.batch_create(otus: {}, ** args)
    new_otus = []
    begin
      Otu.transaction do
        otus.each_key do |k|
          o = Otu.new(otus[k])
          o.save!
          new_otus.push(o)
        end
      end
    rescue
      return false
    end
    new_otus
  end

  # @return [Boolean]
  #   whether or not this otu is coordinate (see coordinate_otus) with this otu
  def coordinate_with?(otu_id)
    Otu.coordinate_otus(otu_id).where(otus: {id: id}).any?
  end

  # Hernán - this is extremely hacky, I'd like to
  # map core keys to procs, use yield:, use cached values,
  # add logic for has_many handling (e.g. identifiers) etc.
  # ultmately, each key maps to a proc that returns a value
  #
  # deprecated for new approach in CollectionObject, AssertedDistribution
  def dwca_core
    core = Dwca::GbifProfile::CoreTaxon.new

    core.nomenclaturalCode        = (taxon_name.rank_class.nomenclatural_code.to_s.upcase)
    core.taxonomicStatus          = (taxon_name.unavailable_or_invalid? ? nil : 'accepted')
    core.nomenclaturalStatus      = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking
    core.scientificName           = taxon_name.cached
    core.scientificNameAuthorship = taxon_name.cached_author_year
    core.scientificNameID         = taxon_name.identifiers.first.identifier
    core.taxonRank                = taxon_name.rank
    core.namePublishedIn          = taxon_name.source.cached
    core
  end

  # TODO: Deprecate for helper method, HTML does not belong here
  def otu_name
    if !name.blank?
      name
    elsif !taxon_name_id.nil?
      taxon_name.cached_html_name_and_author_year
    else
      nil
    end
  end

  # TODO: move to helper method likely
  def distribution_geoJSON
    a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions)
    c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences)
    c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area)
    Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution)
  end

  # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        when 'Content'
          Content.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        else
          return Otu.none
        end

    p = Otu.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_object_type'].eq('Otu')
              )
          )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['otu_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')

    case used_on
        when 'BiologicalAssociation'
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_object_id'].eq(p['id'])
          ))
        else
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id'])))
        end

    Otu.joins(j).pluck(:id).uniq
  end

  # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination'
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

    if target && !r.empty?
      h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a +
          Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now)
              .order('updated_at DESC')
              .limit(3).to_a
              ).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
    else
      h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
    end

    h
  end

  protected

  def check_required_fields
    if taxon_name_id.blank? && name.blank?
      errors.add(:taxon_name_id, 'and/or name should be selected')
      errors.add(:name, 'and/or taxon name should be selected')
    end
  end

  def sv_taxon_name
    soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil?
  end

  def sv_duplicate_otu
    unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty?
      m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project"
      soft_validations.add(:taxon_name_id, m)
      soft_validations.add(:name, m )
    end
  end

end

#taxon_name_id ⇒ Integer

The id of the nomenclatural name for this OTU. The presence of a nomenclatural name carries no biological meaning, it is simply a means to organize concepts within a nomenclatural system.

Returns:

  • (Integer) 


24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
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
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
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
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
 
# File 'app/models/otu.rb', line 24

class Otu < ApplicationRecord
  include Housekeeping
  include SoftValidation
  #include Shared::AlternateValues   # No alternate values on Name!!
  include Shared::Citations          # TODO: have to think hard about this vs. using Nico's framework
  include Shared::DataAttributes
  include Shared::Identifiers
  include Shared::Notes
  include Shared::Tags
  include Shared::Depictions
  include Shared::Loanable
  include Shared::Confidences
  include Shared::Observations
  include Shared::BiologicalAssociations
  include Shared::HasPapertrail
  include Shared::OriginRelationship

  include Shared::MatrixHooks::Member
  include Otu::MatrixHooks

  include Shared::IsData

  is_origin_for 'Sequence', 'Extract'

  GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations]

  belongs_to :taxon_name, inverse_of: :otus

  has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error

  has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error
  has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error

  has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change
  has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus

  has_many :extracts, through: :collection_objects, source: :extracts
  has_many :sequences, through: :extracts, source: :derived_sequences

  has_many :collecting_events, -> { distinct }, through: :collection_objects
  has_many :common_names, dependent: :destroy
  has_many :collection_profiles, dependent: :restrict_with_error  # @proceps dependent: what?
  has_many :contents, inverse_of: :otu, dependent: :destroy
  has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area
  has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area
  has_many :georeferences, through: :collecting_events

  has_many :content_topics, through: :contents, source: :topic

  has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu'
  has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all
  has_many :observation_matrices, through: :observation_matrix_rows

  has_many :observations, inverse_of: :otu, dependent: :restrict_with_error
  has_many :descriptors, through: :observations

  scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) }
  scope :with_name, -> (name) { where(name: name) }

  # @return Scope
  def self.alphabetically
    includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC')
  end

  # @param [Integer] otu_id
  # @param [String] rank_class
  # @return [Scope]
  #    Otu.joins(:taxon_name).where(taxon_name: q).to_sql
  def self.self_and_descendants_of(otu_id, rank_class = nil)
    if o = Otu.joins(:taxon_name).find(otu_id)
      if rank_class.nil?
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants)
      else
        joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class))
      end
    else # no taxon name just return self in scope
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #
  # All OTUs that are synonymous/same/matching target, for either
  #    historical and pragmatic (i.e. share the same `taxon_name_id`), or
  #    nomenclatural reasons (are synonyms of the taxon name). Includes self.
  #
  def self.coordinate_otus(otu_id)
    begin
      i = Otu.joins(:taxon_name).find(otu_id)
      j = i.taxon_name.cached_valid_taxon_name_id
      o = Otu.arel_table
      t = TaxonName.arel_table

      q = o.join(t, Arel::Nodes::InnerJoin).on(
        o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j))
      )

      Otu.joins(q.join_sources)
    rescue ActiveRecord::RecordNotFound
      Otu.where(id: otu_id)
    end
  end

  # @return [Otu::ActiveRecordRelation]
  #   if the Otu is a child, via synonymy or not, of the taxon name
  #   !! Invalid taxon_name_ids return nothing
  #   !! Taxon names with synonyms return the OTUs of their synonyms
  def self.descendant_of_taxon_name(taxon_name_id)
    o = Otu.arel_table
    t = TaxonName.arel_table
    h = TaxonNameHierarchy.arel_table

    q = o.join(t, Arel::Nodes::InnerJoin).on(
      o[:taxon_name_id].eq( t[:id]))
      .join(h, Arel::Nodes::InnerJoin).on(
        t[:cached_valid_taxon_name_id].eq(h[:descendant_id]))

    Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql)
  end

  def current_collection_objects
    collection_objects.where(taxon_determinations: {position: 1})
  end

  validate :check_required_fields

  soft_validate(:sv_taxon_name, set: :taxon_name)
  soft_validate(:sv_duplicate_otu, set: :duplicate_otu)

  accepts_nested_attributes_for :common_names, allow_destroy: true

  # @return [Otu#id, nil, false]
  #  nil - there is no OTU parent with a valid taxon name possible
  #  false - there is > 1 OTU parent with a valid taxon name possible
  #  id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name
  #
  #  Note this is used CoLDP export. Do not change without considerations there.
  def parent_otu_id
    return nil if taxon_name_id.nil?

    # TODO: Unify to a single query

    candidates = TaxonName.joins(:otus, :descendant_hierarchies)
      .that_is_valid
      .where.not(id: taxon_name_id)
      .where(taxon_name_hierarchies: {descendant_id: taxon_name_id})
      .order('taxon_name_hierarchies.generations')
      .limit(1)
      .pluck(:id)

    if candidates.size == 1
      otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load
      if otus.size == 1
        return otus.first.id
      elsif otus.count > 1
        return false
      else
      return nil
      end
    else
      return nil
    end
  end

  # @return [Array]
  #   all bilogical associations this Otu is part of
  def all_biological_associations
    # !! If self relationships are ever made possible this needs a DISTINCT clause
    BiologicalAssociation.find_by_sql(
      "SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_subject_id = #{self.id}
           AND biological_associations.biological_association_subject_type = 'Otu'
       UNION
       SELECT biological_associations.*
         FROM biological_associations
         WHERE biological_associations.biological_association_object_id = #{self.id}
           AND biological_associations.biological_association_object_type = 'Otu' ")
  end

  # return [Scope] the Otus bound to that taxon name and its descendants
  def self.for_taxon_name(taxon_name)
    if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer)
      tn = TaxonName.find(taxon_name)
    else
      tn = taxon_name
    end
    Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id})
  end

  # TODO: This need to be renamed to reflect "simple" association
  def self.batch_preview(file: nil, ** args)
    # f     = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol)
    @otus = []
    File.open(file).each do |row|
      name = row.strip
      next if name.blank?
      @otus.push(Otu.new(name: row.strip))
    end
    @otus
  end

  def self.batch_create(otus: {}, ** args)
    new_otus = []
    begin
      Otu.transaction do
        otus.each_key do |k|
          o = Otu.new(otus[k])
          o.save!
          new_otus.push(o)
        end
      end
    rescue
      return false
    end
    new_otus
  end

  # @return [Boolean]
  #   whether or not this otu is coordinate (see coordinate_otus) with this otu
  def coordinate_with?(otu_id)
    Otu.coordinate_otus(otu_id).where(otus: {id: id}).any?
  end

  # Hernán - this is extremely hacky, I'd like to
  # map core keys to procs, use yield:, use cached values,
  # add logic for has_many handling (e.g. identifiers) etc.
  # ultmately, each key maps to a proc that returns a value
  #
  # deprecated for new approach in CollectionObject, AssertedDistribution
  def dwca_core
    core = Dwca::GbifProfile::CoreTaxon.new

    core.nomenclaturalCode        = (taxon_name.rank_class.nomenclatural_code.to_s.upcase)
    core.taxonomicStatus          = (taxon_name.unavailable_or_invalid? ? nil : 'accepted')
    core.nomenclaturalStatus      = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking
    core.scientificName           = taxon_name.cached
    core.scientificNameAuthorship = taxon_name.cached_author_year
    core.scientificNameID         = taxon_name.identifiers.first.identifier
    core.taxonRank                = taxon_name.rank
    core.namePublishedIn          = taxon_name.source.cached
    core
  end

  # TODO: Deprecate for helper method, HTML does not belong here
  def otu_name
    if !name.blank?
      name
    elsif !taxon_name_id.nil?
      taxon_name.cached_html_name_and_author_year
    else
      nil
    end
  end

  # TODO: move to helper method likely
  def distribution_geoJSON
    a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions)
    c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences)
    c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area)
    Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution)
  end

  # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    t = case used_on
        when 'AssertedDistribution'
          AssertedDistribution.arel_table
        when 'Content'
          Content.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        else
          return Otu.none
        end

    p = Otu.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_object_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_object_type'].eq('Otu')
              )
          )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['otu_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    z = i.as('recent_t')

    case used_on
        when 'BiologicalAssociation'
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_object_id'].eq(p['id'])
          ))
        else
          j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id'])))
        end

    Otu.joins(j).pluck(:id).uniq
  end

  # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination'
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

    if target && !r.empty?
      h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a +
          Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now)
              .order('updated_at DESC')
              .limit(3).to_a
              ).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
    else
      h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
      h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
    end

    h
  end

  protected

  def check_required_fields
    if taxon_name_id.blank? && name.blank?
      errors.add(:taxon_name_id, 'and/or name should be selected')
      errors.add(:name, 'and/or taxon name should be selected')
    end
  end

  def sv_taxon_name
    soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil?
  end

  def sv_duplicate_otu
    unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty?
      m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project"
      soft_validations.add(:taxon_name_id, m)
      soft_validations.add(:name, m )
    end
  end

end

Class Method Details

.alphabetically ⇒ Object

Returns Scope.

Returns:

  • Scope



84
85
86
 
# File 'app/models/otu.rb', line 84

def self.alphabetically
  includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC')
end

.batch_create(otus: {}, **args) ⇒ Object 



226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
 
# File 'app/models/otu.rb', line 226

def self.batch_create(otus: {}, ** args)
  new_otus = []
  begin
    Otu.transaction do
      otus.each_key do |k|
        o = Otu.new(otus[k])
        o.save!
        new_otus.push(o)
      end
    end
  rescue
    return false
  end
  new_otus
end

.batch_preview(file: nil, **args) ⇒ Object

TODO: This need to be renamed to reflect “simple” association



215
216
217
218
219
220
221
222
223
224
 
# File 'app/models/otu.rb', line 215

def self.batch_preview(file: nil, ** args)
  # f     = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol)
  @otus = []
  File.open(file).each do |row|
    name = row.strip
    next if name.blank?
    @otus.push(Otu.new(name: row.strip))
  end
  @otus
end

.coordinate_otus(otu_id) ⇒ Otu::ActiveRecordRelation

All OTUs that are synonymous/same/matching target, for either

historical and pragmatic (i.e. share the same `taxon_name_id`), or
nomenclatural reasons (are synonyms of the taxon name). Includes self.

Returns:

  • (Otu::ActiveRecordRelation) 


110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
 
# File 'app/models/otu.rb', line 110

def self.coordinate_otus(otu_id)
  begin
    i = Otu.joins(:taxon_name).find(otu_id)
    j = i.taxon_name.cached_valid_taxon_name_id
    o = Otu.arel_table
    t = TaxonName.arel_table

    q = o.join(t, Arel::Nodes::InnerJoin).on(
      o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j))
    )

    Otu.joins(q.join_sources)
  rescue ActiveRecord::RecordNotFound
    Otu.where(id: otu_id)
  end
end

.descendant_of_taxon_name(taxon_name_id) ⇒ Otu::ActiveRecordRelation

Returns if the Otu is a child, via synonymy or not, of the taxon name !! Invalid taxon_name_ids return nothing !! Taxon names with synonyms return the OTUs of their synonyms.

Returns:

  • (Otu::ActiveRecordRelation) —

    if the Otu is a child, via synonymy or not, of the taxon name !! Invalid taxon_name_ids return nothing !! Taxon names with synonyms return the OTUs of their synonyms



131
132
133
134
135
136
137
138
139
140
141
142
 
# File 'app/models/otu.rb', line 131

def self.descendant_of_taxon_name(taxon_name_id)
  o = Otu.arel_table
  t = TaxonName.arel_table
  h = TaxonNameHierarchy.arel_table

  q = o.join(t, Arel::Nodes::InnerJoin).on(
    o[:taxon_name_id].eq( t[:id]))
    .join(h, Arel::Nodes::InnerJoin).on(
      t[:cached_valid_taxon_name_id].eq(h[:descendant_id]))

  Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql)
end

.for_taxon_name(taxon_name) ⇒ Object

return [Scope] the Otus bound to that taxon name and its descendants



205
206
207
208
209
210
211
212
 
# File 'app/models/otu.rb', line 205

def self.for_taxon_name(taxon_name)
  if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer)
    tn = TaxonName.find(taxon_name)
  else
    tn = taxon_name
  end
  Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id})
end

.select_optimized(user_id, project_id, target = nil) ⇒ Hash

Returns otus optimized for user selection.

Returns:

  • (Hash) —

    otus optimized for user selection



342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
 
# File 'app/models/otu.rb', line 342

def self.select_optimized(user_id, project_id, target = nil)
  r = used_recently(user_id, project_id, target)
  h = {
    quick: [],
    pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a,
    recent: []
  }

  if target && !r.empty?
    h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a +
        Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now)
            .order('updated_at DESC')
            .limit(3).to_a
            ).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
    h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
        Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
  else
    h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
    h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
  end

  h
end

.self_and_descendants_of(otu_id, rank_class = nil) ⇒ Scope

Returns Otu.joins(:taxon_name).where(taxon_name: q).to_sql.

Parameters:

  • otu_id (Integer)
  • rank_class (String) (defaults to: nil)

Returns:

  • (Scope) —

    Otu.joins(:taxon_name).where(taxon_name: q).to_sql



92
93
94
95
96
97
98
99
100
101
102
 
# File 'app/models/otu.rb', line 92

def self.self_and_descendants_of(otu_id, rank_class = nil)
  if o = Otu.joins(:taxon_name).find(otu_id)
    if rank_class.nil?
      joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants)
    else
      joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class))
    end
  else # no taxon name just return self in scope
    Otu.where(id: otu_id)
  end
end

.used_recently(user_id, project_id, used_on = '') ⇒ Scope

Returns the max 10 most recently used otus, as `used_on`.

Parameters:

  • used_on (String) (defaults to: '') —

    required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination`

Returns:

  • (Scope) —

    the max 10 most recently used otus, as `used_on`



290
291
292
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
 
# File 'app/models/otu.rb', line 290

def self.used_recently(user_id, project_id, used_on = '')
  t = case used_on
      when 'AssertedDistribution'
        AssertedDistribution.arel_table
      when 'Content'
        Content.arel_table
      when 'BiologicalAssociation'
        BiologicalAssociation.arel_table
      when 'TaxonDetermination'
        TaxonDetermination.arel_table
      else
        return Otu.none
      end

  p = Otu.arel_table

  # i is a select manager
  i = case used_on
      when 'BiologicalAssociation'
        t.project(t['biological_association_object_id'], t['updated_at']).from(t)
          .where(
            t['updated_at'].gt(1.weeks.ago).and(
              t['biological_association_object_type'].eq('Otu')
            )
        )
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      else
        t.project(t['otu_id'], t['updated_at']).from(t)
          .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      end

  z = i.as('recent_t')

  case used_on
      when 'BiologicalAssociation'
        j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
          z['biological_association_object_id'].eq(p['id'])
        ))
      else
        j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id'])))
      end

  Otu.joins(j).pluck(:id).uniq
end

Instance Method Details

#all_biological_associations ⇒ Array

Returns all bilogical associations this Otu is part of.

Returns:

  • (Array) —

    all bilogical associations this Otu is part of



190
191
192
193
194
195
196
197
198
199
200
201
202
 
# File 'app/models/otu.rb', line 190

def all_biological_associations
  # !! If self relationships are ever made possible this needs a DISTINCT clause
  BiologicalAssociation.find_by_sql(
    "SELECT biological_associations.*
       FROM biological_associations
       WHERE biological_associations.biological_association_subject_id = #{self.id}
         AND biological_associations.biological_association_subject_type = 'Otu'
     UNION
     SELECT biological_associations.*
       FROM biological_associations
       WHERE biological_associations.biological_association_object_id = #{self.id}
         AND biological_associations.biological_association_object_type = 'Otu' ")
end

#check_required_fields ⇒ Object (protected) 



368
369
370
371
372
373
 
# File 'app/models/otu.rb', line 368

def check_required_fields
  if taxon_name_id.blank? && name.blank?
    errors.add(:taxon_name_id, 'and/or name should be selected')
    errors.add(:name, 'and/or taxon name should be selected')
  end
end

#coordinate_with?(otu_id) ⇒ Boolean

Returns whether or not this otu is coordinate (see coordinate_otus) with this otu.

Returns:

  • (Boolean) —

    whether or not this otu is coordinate (see coordinate_otus) with this otu



244
245
246
 
# File 'app/models/otu.rb', line 244

def coordinate_with?(otu_id)
  Otu.coordinate_otus(otu_id).where(otus: {id: id}).any?
end

#current_collection_objects ⇒ Object 



144
145
146
 
# File 'app/models/otu.rb', line 144

def current_collection_objects
  collection_objects.where(taxon_determinations: {position: 1})
end

#distribution_geoJSON ⇒ Object

TODO: move to helper method likely



280
281
282
283
284
285
 
# File 'app/models/otu.rb', line 280

def distribution_geoJSON
  a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions)
  c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences)
  c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area)
  Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution)
end

#dwca_core ⇒ Object

Hernán - this is extremely hacky, I'd like to map core keys to procs, use yield:, use cached values, add logic for has_many handling (e.g. identifiers) etc. ultmately, each key maps to a proc that returns a value

deprecated for new approach in CollectionObject, AssertedDistribution



254
255
256
257
258
259
260
261
262
263
264
265
266
 
# File 'app/models/otu.rb', line 254

def dwca_core
  core = Dwca::GbifProfile::CoreTaxon.new

  core.nomenclaturalCode        = (taxon_name.rank_class.nomenclatural_code.to_s.upcase)
  core.taxonomicStatus          = (taxon_name.unavailable_or_invalid? ? nil : 'accepted')
  core.nomenclaturalStatus      = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking
  core.scientificName           = taxon_name.cached
  core.scientificNameAuthorship = taxon_name.cached_author_year
  core.scientificNameID         = taxon_name.identifiers.first.identifier
  core.taxonRank                = taxon_name.rank
  core.namePublishedIn          = taxon_name.source.cached
  core
end

#otu_name ⇒ Object

TODO: Deprecate for helper method, HTML does not belong here



269
270
271
272
273
274
275
276
277
 
# File 'app/models/otu.rb', line 269

def otu_name
  if !name.blank?
    name
  elsif !taxon_name_id.nil?
    taxon_name.cached_html_name_and_author_year
  else
    nil
  end
end

#parent_otu_id ⇒ Otu#id, ...

Returns nil - there is no OTU parent with a valid taxon name possible false - there is > 1 OTU parent with a valid taxon name possible id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name

Note this is used CoLDP export. Do not change without considerations there.

Returns:

  • (Otu#id, nil, false) —

    nil - there is no OTU parent with a valid taxon name possible false - there is > 1 OTU parent with a valid taxon name possible id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name

    Note this is used CoLDP export. Do not change without considerations there.



161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
 
# File 'app/models/otu.rb', line 161

def parent_otu_id
  return nil if taxon_name_id.nil?

  # TODO: Unify to a single query

  candidates = TaxonName.joins(:otus, :descendant_hierarchies)
    .that_is_valid
    .where.not(id: taxon_name_id)
    .where(taxon_name_hierarchies: {descendant_id: taxon_name_id})
    .order('taxon_name_hierarchies.generations')
    .limit(1)
    .pluck(:id)

  if candidates.size == 1
    otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load
    if otus.size == 1
      return otus.first.id
    elsif otus.count > 1
      return false
    else
    return nil
    end
  else
    return nil
  end
end

#sv_duplicate_otu ⇒ Object (protected) 



379
380
381
382
383
384
385
 
# File 'app/models/otu.rb', line 379

def sv_duplicate_otu
  unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty?
    m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project"
    soft_validations.add(:taxon_name_id, m)
    soft_validations.add(:name, m )
  end
end

#sv_taxon_name ⇒ Object (protected) 



375
376
377
 
# File 'app/models/otu.rb', line 375

def sv_taxon_name
  soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil?
end