Class: Citation

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::BiologicalAssociationIndexHooks, Shared::IsData, Shared::Notes, Shared::PolymorphicAnnotator, Shared::Tags, SoftValidation
Defined in:
app/models/citation.rb

Overview

A Citation is an assertion that the subject (i.e. citation object/record/data instance), or some attribute of it, was referenced or originated in a Source.

Constant Summary collapse

IGNORE_IDENTICAL =

unify's dedup logic resets is_original to false on a would-be duplicate before comparing it to the surviving Citation via #identical; if is_original weren't ignored here that reset would make the two look different and the duplicate would never be matched.

[:is_original].freeze

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

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 Shared::PolymorphicAnnotator

#annotated_object_is_persisted?

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_in_use?, #similar

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 Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#citation_object_id ⇒ Integer

Returns Rails STI, the id of the object being cited.

Returns:

  • (Integer) —

    Rails STI, the id of the object being cited



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

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

end

#citation_object_type ⇒ String

Returns Rails STI, the class of the object being cited.

Returns:

  • (String) —

    Rails STI, the class of the object being cited



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

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

end

#is_original ⇒ Boolean

Returns is this the first citation in which the data were observed?.

Returns:

  • (Boolean) —

    is this the first citation in which the data were observed?



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

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

end

#no_cached ⇒ Object

Returns the value of attribute no_cached.



41
42
43
 
# File 'app/models/citation.rb', line 41

def no_cached
  @no_cached
end

#pages ⇒ String?

Returns a specific location/localization for the data in the Source, if you lead with an integer separated by space or punctation that integer will be returned as the "first" page and usable in direct linkouts to Documents if available.

Returns:

  • (String, nil) —

    a specific location/localization for the data in the Source, if you lead with an integer separated by space or punctation that integer will be returned as the "first" page and usable in direct linkouts to Documents if available



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

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

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

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

end

#source_id ⇒ Integer

the source 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
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
 
# File 'app/models/citation.rb', line 29

class Citation < ApplicationRecord

  # Citations do not have Confidence or DataAttribute.

  include Housekeeping
  include Shared::Notes
  include Shared::Tags
  include Shared::IsData
  include Shared::PolymorphicAnnotator
  include Shared::BiologicalAssociationIndexHooks
  include SoftValidation

  attr_accessor :no_cached

  # unify's dedup logic resets is_original to false on a would-be duplicate
  # before comparing it to the surviving Citation via #identical; if
  # is_original weren't ignored here that reset would make the two look
  # different and the duplicate would never be matched.
  IGNORE_IDENTICAL = [:is_original].freeze

  polymorphic_annotates('citation_object')

  # belongs_to :source, inverse_of: :origin_citations
  belongs_to :source, inverse_of: :citations

  has_many :citation_topics, inverse_of: :citation, dependent: :destroy
  has_many :topics, through: :citation_topics, inverse_of: :citations
  has_many :documents, through: :source

  validates_presence_of :source

  validates_uniqueness_of :source_id, scope: [:citation_object_id, :citation_object_type, :pages]
  validates_uniqueness_of :is_original, scope: [:citation_object_type, :citation_object_id], message: 'can only be assigned once per object.', allow_nil: true, if: -> { is_original? }

  accepts_nested_attributes_for :citation_topics, allow_destroy: true, reject_if: :reject_citation_topics
  accepts_nested_attributes_for :topics, allow_destroy: true, reject_if: :reject_topic

  before_destroy :prevent_if_required

  after_create :add_source_to_project

  before_save {@old_is_original = is_original_was}
  before_save {@old_citation_object_id = citation_object_id_was}
  before_save {@old_source_id = source_id_was}

  after_save :update_related_cached_values, if: :is_original?

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  soft_validate(:sv_page_range, set: :page_range)

  def self.batch_create(params)
    ids = params[:citation_object_id]
    params.delete(:citation_object_id)

    citations = []
    Citation.transaction do
      begin
        ids.each do |id|
          citations.push Citation.create!(
            params.merge(
              citation_object_id: id
            )
          )
        end
      rescue ActiveRecord::RecordInvalid
        return false
      end
    end
    citations
  end

  # TODO: deprecate
  # @return [Scope of matching sources]
  def self.find_for_autocomplete(params)
    term = params['term']
    ending = term + '%'
    wrapped = '%' + term + '%'
    joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
  end

  # @return [Boolean]
  #   true if is_original is checked, false if nil/false
  def is_original?
    is_original ? true : false
  end

  # @return [String, nil]
  #    the first integer in the string, as a string
  def first_page
    /(?<i>\d+)/ =~ pages
    i
  end

  # @return [Integer, nil]
  #    if a target document
  def target_document_page
    target_document.try(:pdf_page_for, first_page).try(:first)
  end

  # @return [Document, nil]
  def target_document
    documents.order('documentation.position').first
  end

  # @return [ActiveRecord::Relation]
  #   BiologicalAssociationIndex records for the association cited by this citation
  def biological_association_indices
    return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

    BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
  end

  protected

  def add_source_to_project
    !!ProjectSource.find_or_create_by(project:, source:)
  end

  def reject_citation_topics(attributed)
    attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
  end

  def reject_topic(attributed)
    attributed['name'].blank? || attributed['definition'].blank?
  end

  def update_related_cached_values
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonName'
        citation_object.update_columns(
          cached_author_year: citation_object.get_author_and_year,
          cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
      end
    end
    true
  end

  def prevent_if_required
    # Note this ignores nested _destroys; for rails reasons we do that on
    # the parent instead, where everything 'just works'.
    return if marked_for_destruction?
    return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

    # Allow the destroy if citation_object itself is already committed to
    # being destroyed by an enclosing Shared::Unify#unify call - it's not
    # losing its last citation, it's going away entirely, so the "must have
    # at least one citation" guard below is moot.
    return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
      { id: citation_object.id, type: citation_object.class.base_class.name }
    )

    if citation_object.requires_citation? && citation_object.citations.count == 1
      errors.add(:base, 'at least one citation is required')
      throw(:abort)
    end
  end

  def set_cached_names_for_taxon_names
    if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
      if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
        begin
          TaxonNameRelationship.transaction do
            t = citation_object.subject_taxon_name
            vn = t.get_valid_taxon_name

            n = t.get_full_name

            t.update_columns(
              cached: n,
              cached_html: t.get_full_name_html(n),
              cached_valid_taxon_name_id: vn.id)

            # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
            t.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end

            vn.list_of_invalid_taxon_names.each do |s|
              s.update_column(:cached_valid_taxon_name_id, vn.id)
              s.combination_list_self.each do |c|
                c.update_column(:cached_valid_taxon_name_id, vn.id)
              end
            end
          end
        rescue ActiveRecord::RecordInvalid
          raise
        end
        false
      end
    end
  end

  def sv_page_range
    if pages.blank?
      soft_validations.add(:pages, 'Citation pages are not provided')
    elsif source.pages.present?
      matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if matchdata1
        citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
        citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
        matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
        if citMinP && citMaxP && matchdata
          minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
          maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
          minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
          unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
            soft_validations.add(:pages, 'Citation is out of the source page range')
          end
        end
      end
    end
  end

end

Class Method Details

.batch_create(params) ⇒ Object 



81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
 
# File 'app/models/citation.rb', line 81

def self.batch_create(params)
  ids = params[:citation_object_id]
  params.delete(:citation_object_id)

  citations = []
  Citation.transaction do
    begin
      ids.each do |id|
        citations.push Citation.create!(
          params.merge(
            citation_object_id: id
          )
        )
      end
    rescue ActiveRecord::RecordInvalid
      return false
    end
  end
  citations
end

.find_for_autocomplete(params) ⇒ Scope of matching sources

TODO: deprecate

Returns:

  • (Scope of matching sources) 


104
105
106
107
108
109
 
# File 'app/models/citation.rb', line 104

def self.find_for_autocomplete(params)
  term = params['term']
  ending = term + '%'
  wrapped = '%' + term + '%'
  joins(:source).where('sources.cached ILIKE ? OR sources.cached ILIKE ? OR citation_object_type LIKE ?', ending, wrapped, ending).with_project_id(params[:project_id])
end

Instance Method Details

#add_source_to_project ⇒ Object (protected) 



145
146
147
 
# File 'app/models/citation.rb', line 145

def add_source_to_project
  !!ProjectSource.find_or_create_by(project:, source:)
end

#biological_association_indices ⇒ ActiveRecord::Relation

Returns BiologicalAssociationIndex records for the association cited by this citation.

Returns:

  • (ActiveRecord::Relation) —

    BiologicalAssociationIndex records for the association cited by this citation



137
138
139
140
141
 
# File 'app/models/citation.rb', line 137

def biological_association_indices
  return BiologicalAssociationIndex.none unless citation_object_type == 'BiologicalAssociation'

  BiologicalAssociationIndex.where(biological_association_id: citation_object_id)
end

#first_page ⇒ String?

Returns the first integer in the string, as a string.

Returns:

  • (String, nil) —

    the first integer in the string, as a string



119
120
121
122
 
# File 'app/models/citation.rb', line 119

def first_page
  /(?<i>\d+)/ =~ pages
  i
end

#is_original? ⇒ Boolean

Returns true if is_original is checked, false if nil/false.

Returns:

  • (Boolean) —

    true if is_original is checked, false if nil/false



113
114
115
 
# File 'app/models/citation.rb', line 113

def is_original?
  is_original ? true : false
end

#prevent_if_required ⇒ Object (protected) 



168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
 
# File 'app/models/citation.rb', line 168

def prevent_if_required
  # Note this ignores nested _destroys; for rails reasons we do that on
  # the parent instead, where everything 'just works'.
  return if marked_for_destruction?
  return if citation_object && citation_object.respond_to?(:ignore_citation_restriction) && citation_object.ignore_citation_restriction

  # Allow the destroy if citation_object itself is already committed to
  # being destroyed by an enclosing Shared::Unify#unify call - it's not
  # losing its last citation, it's going away entirely, so the "must have
  # at least one citation" guard below is moot.
  return if citation_object && UnifyDestroyContext.objects_in_destroy&.include?(
    { id: citation_object.id, type: citation_object.class.base_class.name }
  )

  if citation_object.requires_citation? && citation_object.citations.count == 1
    errors.add(:base, 'at least one citation is required')
    throw(:abort)
  end
end

#reject_citation_topics(attributed) ⇒ Object (protected) 



149
150
151
 
# File 'app/models/citation.rb', line 149

def reject_citation_topics(attributed)
  attributes['id'].blank? && attributed['topic_id'].blank? && attributed['topic'].blank? && attributed['topic_attributes'].blank?
end

#reject_topic(attributed) ⇒ Object (protected) 



153
154
155
 
# File 'app/models/citation.rb', line 153

def reject_topic(attributed)
  attributed['name'].blank? || attributed['definition'].blank?
end

#set_cached_names_for_taxon_names ⇒ Object (protected) 



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

def set_cached_names_for_taxon_names
  if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
    if citation_object_type == 'TaxonNameRelationship' && TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(citation_object.try(:type_name))
      begin
        TaxonNameRelationship.transaction do
          t = citation_object.subject_taxon_name
          vn = t.get_valid_taxon_name

          n = t.get_full_name

          t.update_columns(
            cached: n,
            cached_html: t.get_full_name_html(n),
            cached_valid_taxon_name_id: vn.id)

          # @proceps: This and below is not updating cached names.  Is this required because timing (new dates) may change synonymy?
          t.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end

          vn.list_of_invalid_taxon_names.each do |s|
            s.update_column(:cached_valid_taxon_name_id, vn.id)
            s.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end
          end
        end
      rescue ActiveRecord::RecordInvalid
        raise
      end
      false
    end
  end
end

#sv_page_range ⇒ Object (protected) 



223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
 
# File 'app/models/citation.rb', line 223

def sv_page_range
  if pages.blank?
    soft_validations.add(:pages, 'Citation pages are not provided')
  elsif source.pages.present?
    matchdata1 = pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
    if matchdata1
      citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
      citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i
      matchdata = source.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
      if citMinP && citMaxP && matchdata
        minP = matchdata[1] ? matchdata[1].to_i : matchdata[3].to_i
        maxP = matchdata[2] ? matchdata[2].to_i : matchdata[3].to_i
        minP = 1 if minP == maxP && %w{book booklet manual mastersthesis phdthesis techreport}.include?(source.bibtex_type)
        unless (maxP && minP && minP <= citMinP && maxP >= citMaxP)
          soft_validations.add(:pages, 'Citation is out of the source page range')
        end
      end
    end
  end
end

#target_document ⇒ Document?

Returns:



131
132
133
 
# File 'app/models/citation.rb', line 131

def target_document
  documents.order('documentation.position').first
end

#target_document_page ⇒ Integer?

Returns if a target document.

Returns:

  • (Integer, nil) —

    if a target document



126
127
128
 
# File 'app/models/citation.rb', line 126

def target_document_page
  target_document.try(:pdf_page_for, first_page).try(:first)
end

#update_related_cached_values ⇒ Object (protected) 



157
158
159
160
161
162
163
164
165
166
 
# File 'app/models/citation.rb', line 157

def update_related_cached_values
  if is_original != @old_is_original || citation_object_id != @old_citation_object_id || source_id != @old_source_id
    if citation_object_type == 'TaxonName'
      citation_object.update_columns(
        cached_author_year: citation_object.get_author_and_year,
        cached_nomenclature_date: citation_object.nomenclature_date)  if citation_object.persisted?
    end
  end
  true
end