Class: BiologicalAssociation

Inherits:
ApplicationRecord show all
Includes:
DwcExtensions, GlobiExtensions, Housekeeping, Shared::AutoUuid, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::Depictions, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::QueryBatchUpdate, Shared::Tags, SoftValidation
Defined in:
app/models/biological_association.rb

Overview

A BiologicalAssociation defines a (biological) relationship between two entities. It is an edge in the graph of biological relationships. The relationship can be between two Otus, an Otu and a Collection Object, or between two Collection Objects. For example ‘Species Aus bus is the host_of individual A.’

Defined Under Namespace

Modules: DwcExtensions, GlobiExtensions

Constant Summary

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::QueryBatchUpdate

#query_update

Methods included from DwcExtensions

#darwin_core_extension_json, #darwin_core_extension_row, #dwc_related_resource, #dwc_related_resource_id, #dwc_relationship_according_to, #dwc_relationship_established_date, #dwc_relationship_of_resource, #dwc_relationship_of_resource_id, #dwc_relationship_remarks, #dwc_resource, #dwc_resource_id, #dwc_resource_relationship_id, #globi_extension_json

Methods included from GlobiExtensions

#globi_extension_json, #globi_extension_row, #globi_interaction_type_id, #globi_interaction_type_name, #globi_source_catalog_number, #globi_source_collection_code, #globi_source_institution_code, #globi_source_life_stage_id, #globi_source_life_stage_name, #globi_source_occurrence_id, #globi_source_sex_id, #globi_source_sex_name, #globi_source_taxon_name, #globi_source_taxon_path, #globi_source_taxon_rank, #globi_target_catalog_number, #globi_target_collection_code, #globi_target_institution_code, #globi_target_life_stage_id, #globi_target_life_stage_name, #globi_target_occurrence_id, #globi_target_sex_id, #globi_target_sex_name, #globi_target_taxon_name, #globi_target_taxon_path, #globi_target_taxon_rank

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 Shared::AutoUuid

#create_object_uuid, #generate_uuid_if_required

Methods included from Shared::Depictions

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

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Identifiers

#dwc_occurrence_id, #identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers, #uri, #uuid

Methods included from Shared::Tags

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

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_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#biological_association_object_id ⇒ Integer

Returns Rails polymorphic, id of the object.

Returns:

  • (Integer) —

    Rails polymorphic, id of the object



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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_object_type ⇒ String

Returns Rails polymorphic, type of the object (e.g. CollectionObject).

Returns:

  • (String) —

    Rails polymorphic, type of the object (e.g. CollectionObject)



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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_subject_id ⇒ Integer

Returns Rails polymorphic, id of the subject of the relationship.

Returns:

  • (Integer) —

    Rails polymorphic, id of the subject of the relationship



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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_association_subject_type ⇒ String

Returns Rails polymorphic, type fo the subject (e.g. Otu).

Returns:

  • (String) —

    Rails polymorphic, type fo the subject (e.g. Otu)



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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#biological_relationship_id ⇒ Integer

Returns the BiologicalRelationship id.

Returns:

  • (Integer) —

    the BiologicalRelationship id



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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#object_global_id ⇒ Object

TODO: this is badly named



71
72
73
 
# File 'app/models/biological_association.rb', line 71

def object_global_id
  @object_global_id
end

#project_id ⇒ Integer

the project ID

Returns:

  • (Integer) 


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
 
# File 'app/models/biological_association.rb', line 29

class BiologicalAssociation < ApplicationRecord
  include Housekeeping
  include SoftValidation
  include Shared::Citations
  include Shared::Tags
  include Shared::Identifiers
  include Shared::DataAttributes
  include Shared::Notes
  include Shared::Confidences
  include Shared::Depictions
  include Shared::AutoUuid
  include Shared::IsData

  include BiologicalAssociation::GlobiExtensions
  include BiologicalAssociation::DwcExtensions

  include Shared::QueryBatchUpdate

  belongs_to :biological_relationship, inverse_of: :biological_associations

  has_many :subject_biological_relationship_types, through: :biological_relationship
  has_many :object_biological_relationship_types, through: :biological_relationship

  has_many :subject_biological_properties, through: :subject_biological_relationship_types, source: :biological_property
  has_many :object_biological_properties, through: :object_biological_relationship_types, source: :biological_property

  belongs_to :biological_association_subject, polymorphic: true, inverse_of: :biological_associations
  belongs_to :biological_association_object, polymorphic: true, inverse_of: :related_biological_associations

  has_many :biological_associations_biological_associations_graphs, inverse_of: :biological_association, dependent: :destroy
  has_many :biological_associations_graphs, through: :biological_associations_biological_associations_graphs, inverse_of: :biological_associations

  validates_presence_of :biological_relationship
  validates_presence_of :biological_association_subject
  validates_presence_of :biological_association_object

  validate :association_is_unique

  validate :biological_association_subject_type_is_allowed
  validate :biological_association_object_type_is_allowed

  attr_accessor :subject_global_id
  attr_accessor :object_global_id # TODO: this is badly named

  attr_accessor :rotate

  def rotate=(value)
    s = self.biological_association_subject
    o = self.biological_association_object

    self.biological_association_subject = o
    self.biological_association_object = s
  end

  def subject_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_subject_id, o.id)
    write_attribute(:biological_association_subject_type, o.metamorphosize.class.name)
  end

  def object_global_id=(value)
    o = GlobalID::Locator.locate(value)
    write_attribute(:biological_association_object_id, o.id)
    write_attribute(:biological_association_object_type, o.metamorphosize.class.name)
  end

  # TODO: Why?! this is just biological_association.biological_association_subject_type
  def subject_class_name
    biological_association_subject.try(:class).base_class.name
  end

  # TODO: Why?! this is just biological_association.biological_association_object_type
  def object_class_name
    biological_association_object.try(:class).base_class.name
  end

  # !! You can not set with this method
  def subject
    biological_association_subject
  end

  # !! You can not set with this method
  def object
    biological_association_object
  end

  class << self

    def set_batch_cap(request)
      a = request.filter
      total = a.all.pluck(:biological_relationship_id).uniq

      cap = 0

      case total.size
      when 1
        cap = 5000
        request.cap_reason = 'Maximum allowed.'
      when 2
        cap = 2000
        request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
      else
        cap = 25
        request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
      end

      request.cap = cap
      request
    end

    def batch_update(params)
      request = QueryBatchRequest.new(
        klass: 'BiologicalAssociation',
        object_filter_params: params[:biological_association_query],
        object_params: params[:biological_association],
        async_cutoff: (params[:async_cutoff] || 26),
        preview: params[:preview]
      )

      set_batch_cap(request)
      query_batch_update(request)
    end

  end

  def dwc_extension_select
    BiologicalAssociation
      .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
      .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
  end

  # @return [ActiveRecord::Relation]
  def targeted_join(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  # @return [ActiveRecord::Relation]
  def targeted_join2(target: 'subject', target_class: ::Otu)
    a = arel_table
    b = target_class.arel_table

    j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  end

  # Not used
  # @return [ActiveRecord::Relation]
  def targeted_left_join(target: 'subject', target_class: ::Otu )
    a = arel_table
    b = target_class.arel_table

    j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
    joins(j.join_sources)
  end

  private

  # We need to add the error to the polymorphic object class for Unify puproses, not the subject_id.
  # We can't (apparently) validate uniqueness of a polymorphic with other polymorphic scope.
  def association_is_unique
    if a = BiologicalAssociation.where.not(id:).where(
        biological_association_subject:,
        biological_association_object:,
        biological_relationship:
    ).first
      if a.biological_association_subject == self
        errors.add(:biological_association_subject, "has already been taken")
      else
        errors.add(:biological_association_object, "has already been taken")
      end
    end
  end


  def biological_association_subject_type_is_allowed
    errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
  end

  def biological_association_object_type_is_allowed
    errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
  end
end

#rotate ⇒ Object

Returns the value of attribute rotate.



73
74
75
 
# File 'app/models/biological_association.rb', line 73

def rotate
  @rotate
end

#subject_global_id ⇒ Object

Returns the value of attribute subject_global_id.



70
71
72
 
# File 'app/models/biological_association.rb', line 70

def subject_global_id
  @subject_global_id
end

Class Method Details

.batch_update(params) ⇒ Object 



139
140
141
142
143
144
145
146
147
148
149
150
 
# File 'app/models/biological_association.rb', line 139

def batch_update(params)
  request = QueryBatchRequest.new(
    klass: 'BiologicalAssociation',
    object_filter_params: params[:biological_association_query],
    object_params: params[:biological_association],
    async_cutoff: (params[:async_cutoff] || 26),
    preview: params[:preview]
  )

  set_batch_cap(request)
  query_batch_update(request)
end

.set_batch_cap(request) ⇒ Object 



117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
 
# File 'app/models/biological_association.rb', line 117

def set_batch_cap(request)
  a = request.filter
  total = a.all.pluck(:biological_relationship_id).uniq

  cap = 0

  case total.size
  when 1
    cap = 5000
    request.cap_reason = 'Maximum allowed.'
  when 2
    cap = 2000
    request.cap_reason = 'Maximum allowed when 2 biological relationships present.'
  else
    cap = 25
    request.cap_reason = 'Maximum allowed when 3 or more biological relationships present.'
  end

  request.cap = cap
  request
end

Instance Method Details

#association_is_unique ⇒ Object (private)

We need to add the error to the polymorphic object class for Unify puproses, not the subject_id. We can’t (apparently) validate uniqueness of a polymorphic with other polymorphic scope.



192
193
194
195
196
197
198
199
200
201
202
203
204
 
# File 'app/models/biological_association.rb', line 192

def association_is_unique
  if a = BiologicalAssociation.where.not(id:).where(
      biological_association_subject:,
      biological_association_object:,
      biological_relationship:
  ).first
    if a.biological_association_subject == self
      errors.add(:biological_association_subject, "has already been taken")
    else
      errors.add(:biological_association_object, "has already been taken")
    end
  end
end

#biological_association_object_type_is_allowed ⇒ Object (private) 



211
212
213
 
# File 'app/models/biological_association.rb', line 211

def biological_association_object_type_is_allowed
  errors.add(:biological_association_object_type, 'is not permitted') unless biological_association_object && biological_association_object.class.is_biologically_relatable?
end

#biological_association_subject_type_is_allowed ⇒ Object (private) 



207
208
209
 
# File 'app/models/biological_association.rb', line 207

def biological_association_subject_type_is_allowed
  errors.add(:biological_association_subject_type, 'is not permitted') unless biological_association_subject && biological_association_subject.class.is_biologically_relatable?
end

#dwc_extension_select ⇒ Object 



154
155
156
157
158
159
 
# File 'app/models/biological_association.rb', line 154

def dwc_extension_select
  BiologicalAssociation
    .joins("LEFT JOIN identifiers id_s ON id_s.identifier_object_type = biological_associations.biological_associations_subject_type AND ids_s.type = 'Identifier::Global::Uuid'" )
    .joins("LEFT JOIN identifiers id_o ON id_o.identifier_object_type = biological_associations.biological_associations_object_type AND ids_o.type = 'Identifier::Global::Uuid'" )
    .joins("LEFT JOIN identifiers id_r ON id_o.identifier_object_type = 'BiologicalRelationship' AND idr_.identifier_object_id = biological_associations.biological_relationship_id AND ids_r.type = 'Identifier::Global::Uri'" )
end

#object ⇒ Object

!! You can not set with this method



111
112
113
 
# File 'app/models/biological_association.rb', line 111

def object
  biological_association_object
end

#object_class_name ⇒ Object

TODO: Why?! this is just biological_association.biological_association_object_type



101
102
103
 
# File 'app/models/biological_association.rb', line 101

def object_class_name
  biological_association_object.try(:class).base_class.name
end

#subject ⇒ Object

!! You can not set with this method



106
107
108
 
# File 'app/models/biological_association.rb', line 106

def subject
  biological_association_subject
end

#subject_class_name ⇒ Object

TODO: Why?! this is just biological_association.biological_association_subject_type



96
97
98
 
# File 'app/models/biological_association.rb', line 96

def subject_class_name
  biological_association_subject.try(:class).base_class.name
end

#targeted_join(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


162
163
164
165
166
167
168
 
# File 'app/models/biological_association.rb', line 162

def targeted_join(target: 'subject', target_class: ::Otu)
  a = arel_table
  b = target_class.arel_table

  j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  joins(j.join_sources)
end

#targeted_join2(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


171
172
173
174
175
176
 
# File 'app/models/biological_association.rb', line 171

def targeted_join2(target: 'subject', target_class: ::Otu)
  a = arel_table
  b = target_class.arel_table

  j = a.join(b).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
end

#targeted_left_join(target: 'subject', target_class: ::Otu) ⇒ ActiveRecord::Relation

Not used

Returns:

  • (ActiveRecord::Relation) 


180
181
182
183
184
185
186
 
# File 'app/models/biological_association.rb', line 180

def targeted_left_join(target: 'subject', target_class: ::Otu )
  a = arel_table
  b = target_class.arel_table

  j = a.join(b, Arel::Nodes::OuterJoin).on(a["biological_association_#{target}_type".to_sym].eq(target_class.name).and(a["biological_assoication_#{target}_id".to_sym].eq(b[:id])))
  joins(j.join_sources)
end