Class: Otu
- Inherits:
-
ApplicationRecord
- Object
- ActiveRecord::Base
- ApplicationRecord
- Otu
- Includes:
- Housekeeping, MatrixHooks, Shared::BiologicalAssociations, Shared::Citations, Shared::Confidences, Shared::DataAttributes, Shared::Depictions, Shared::HasPapertrail, Shared::Identifiers, Shared::IsData, Shared::Loanable, Shared::MatrixHooks::Member, Shared::Notes, Shared::Observations, Shared::OriginRelationship, Shared::Tags, SoftValidation
- Defined in:
- app/models/otu.rb
Overview
An Otu (loosely, operational taxonomic unit) can be thought of as a unit of study. In most cases an otu is a taxon.
An Otu is defined by its underlying data and may be labeled with a name (TaxonName). Otus are used to represent rows in matrices, taxon pages, individuals or populations, or arbitrary clusters of organisms (e.g. 'unsorted specimens in this container'). Otus are a primary unit of work in TaxonWorks.
OTU is labeled with a name, either arbitrarily given or specifically linked to a taxon_name_id.
TODO Semantics vs. taxon_name_id
Defined Under Namespace
Modules: MatrixHooks Classes: Autocomplete, Filter
Constant Summary collapse
- GRAPH_ENTRY_POINTS =
[:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations]
Constants included from SoftValidation
SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS
Instance Attribute Summary collapse
-
#name ⇒ String
A label for the OTU.
-
#project_id ⇒ Integer
the project ID.
-
#taxon_name_id ⇒ Integer
The id of the nomenclatural name for this OTU.
Class Method Summary collapse
-
.alphabetically ⇒ Object
Scope.
- .batch_create(otus: {}, **args) ⇒ Object
-
.batch_preview(file: nil, **args) ⇒ Object
TODO: This need to be renamed to reflect “simple” association.
-
.coordinate_otus(otu_id) ⇒ Otu::ActiveRecordRelation
All OTUs that are synonymous/same/matching target, for either historical and pragmatic (i.e. share the same `taxon_name_id`), or nomenclatural reasons (are synonyms of the taxon name).
-
.descendant_of_taxon_name(taxon_name_id) ⇒ Otu::ActiveRecordRelation
If the Otu is a child, via synonymy or not, of the taxon name !! Invalid taxon_name_ids return nothing !! Taxon names with synonyms return the OTUs of their synonyms.
-
.for_taxon_name(taxon_name) ⇒ Object
return [Scope] the Otus bound to that taxon name and its descendants.
-
.select_optimized(user_id, project_id, target = nil) ⇒ Hash
Otus optimized for user selection.
-
.self_and_descendants_of(otu_id, rank_class = nil) ⇒ Scope
Otu.joins(:taxon_name).where(taxon_name: q).to_sql.
-
.used_recently(user_id, project_id, used_on = '') ⇒ Scope
The max 10 most recently used otus, as `used_on`.
Instance Method Summary collapse
-
#all_biological_associations ⇒ Array
All bilogical associations this Otu is part of.
- #check_required_fields ⇒ Object protected
-
#coordinate_with?(otu_id) ⇒ Boolean
Whether or not this otu is coordinate (see coordinate_otus) with this otu.
- #current_collection_objects ⇒ Object
-
#distribution_geoJSON ⇒ Object
TODO: move to helper method likely.
-
#dwca_core ⇒ Object
Hernán - this is extremely hacky, I'd like to map core keys to procs, use yield:, use cached values, add logic for has_many handling (e.g. identifiers) etc.
-
#otu_name ⇒ Object
TODO: Deprecate for helper method, HTML does not belong here.
-
#parent_otu_id ⇒ Otu#id, ...
Nil - there is no OTU parent with a valid taxon name possible false - there is > 1 OTU parent with a valid taxon name possible id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name.
- #sv_duplicate_otu ⇒ Object protected
- #sv_taxon_name ⇒ Object protected
Methods included from Shared::IsData
#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar
Methods included from MatrixHooks
#member_of_new_matrix_row_items, #member_of_old_matrix_row_items
Methods included from Shared::MatrixHooks::Member
#member_add_matrix_columns, #member_add_matrix_rows, #member_add_to_matrix_items, #member_of_new_matrix_column_items, #member_of_new_matrix_row_items, #member_of_old_matrix_column_items, #member_of_old_matrix_row_items, #member_remove_from_matrix_items, #member_remove_matrix_columns, #member_remove_matrix_rows, #member_syncronize_matrices, #member_update_matrix_items?
Methods included from Shared::OriginRelationship
#new_objects, #old_objects, #reject_origin_relationships, #set_origin
Methods included from Shared::Confidences
Methods included from Shared::Loanable
#has_been_loaned?, #is_loanable?, #loan_return_date, #on_loan?, #times_loaned
Methods included from Shared::Depictions
#has_depictions?, #image_array=, #reject_depictions, #reject_images
Methods included from Shared::Tags
#reject_tags, #tag_with, #tagged?, #tagged_with?
Methods included from Shared::Notes
#concatenated_notes_string, #reject_notes
Methods included from Shared::Identifiers
#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers
Methods included from Shared::DataAttributes
#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes
Methods included from Shared::Citations
#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id
Methods included from SoftValidation
#clear_soft_validations, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations
Methods included from Housekeeping
#has_polymorphic_relationship?
Methods inherited from ApplicationRecord
Instance Attribute Details
#name ⇒ String
A label for the OTU.
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# File 'app/models/otu.rb', line 24 class Otu < ApplicationRecord include Housekeeping include SoftValidation #include Shared::AlternateValues # No alternate values on Name!! include Shared::Citations # TODO: have to think hard about this vs. using Nico's framework include Shared::DataAttributes include Shared::Identifiers include Shared::Notes include Shared::Tags include Shared::Depictions include Shared::Loanable include Shared::Confidences include Shared::Observations include Shared::BiologicalAssociations include Shared::HasPapertrail include Shared::OriginRelationship include Shared::MatrixHooks::Member include Otu::MatrixHooks include Shared::IsData is_origin_for 'Sequence', 'Extract' GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations] belongs_to :taxon_name, inverse_of: :otus has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus has_many :extracts, through: :collection_objects, source: :extracts has_many :sequences, through: :extracts, source: :derived_sequences has_many :collecting_events, -> { distinct }, through: :collection_objects has_many :common_names, dependent: :destroy has_many :collection_profiles, dependent: :restrict_with_error # @proceps dependent: what? has_many :contents, inverse_of: :otu, dependent: :destroy has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area has_many :georeferences, through: :collecting_events has_many :content_topics, through: :contents, source: :topic has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu' has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all has_many :observation_matrices, through: :observation_matrix_rows has_many :observations, inverse_of: :otu, dependent: :restrict_with_error has_many :descriptors, through: :observations scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) } scope :with_name, -> (name) { where(name: name) } # @return Scope def self.alphabetically includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC') end # @param [Integer] otu_id # @param [String] rank_class # @return [Scope] # Otu.joins(:taxon_name).where(taxon_name: q).to_sql def self.self_and_descendants_of(otu_id, rank_class = nil) if o = Otu.joins(:taxon_name).find(otu_id) if rank_class.nil? joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants) else joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class)) end else # no taxon name just return self in scope Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # # All OTUs that are synonymous/same/matching target, for either # historical and pragmatic (i.e. share the same `taxon_name_id`), or # nomenclatural reasons (are synonyms of the taxon name). Includes self. # def self.coordinate_otus(otu_id) begin i = Otu.joins(:taxon_name).find(otu_id) j = i.taxon_name.cached_valid_taxon_name_id o = Otu.arel_table t = TaxonName.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j)) ) Otu.joins(q.join_sources) rescue ActiveRecord::RecordNotFound Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # if the Otu is a child, via synonymy or not, of the taxon name # !! Invalid taxon_name_ids return nothing # !! Taxon names with synonyms return the OTUs of their synonyms def self.descendant_of_taxon_name(taxon_name_id) o = Otu.arel_table t = TaxonName.arel_table h = TaxonNameHierarchy.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id])) .join(h, Arel::Nodes::InnerJoin).on( t[:cached_valid_taxon_name_id].eq(h[:descendant_id])) Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql) end def current_collection_objects collection_objects.where(taxon_determinations: {position: 1}) end validate :check_required_fields soft_validate(:sv_taxon_name, set: :taxon_name) soft_validate(:sv_duplicate_otu, set: :duplicate_otu) accepts_nested_attributes_for :common_names, allow_destroy: true # @return [Otu#id, nil, false] # nil - there is no OTU parent with a valid taxon name possible # false - there is > 1 OTU parent with a valid taxon name possible # id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name # # Note this is used CoLDP export. Do not change without considerations there. def parent_otu_id return nil if taxon_name_id.nil? # TODO: Unify to a single query candidates = TaxonName.joins(:otus, :descendant_hierarchies) .that_is_valid .where.not(id: taxon_name_id) .where(taxon_name_hierarchies: {descendant_id: taxon_name_id}) .order('taxon_name_hierarchies.generations') .limit(1) .pluck(:id) if candidates.size == 1 otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load if otus.size == 1 return otus.first.id elsif otus.count > 1 return false else return nil end else return nil end end # @return [Array] # all bilogical associations this Otu is part of def all_biological_associations # !! If self relationships are ever made possible this needs a DISTINCT clause BiologicalAssociation.find_by_sql( "SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_subject_id = #{self.id} AND biological_associations.biological_association_subject_type = 'Otu' UNION SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_object_id = #{self.id} AND biological_associations.biological_association_object_type = 'Otu' ") end # return [Scope] the Otus bound to that taxon name and its descendants def self.for_taxon_name(taxon_name) if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer) tn = TaxonName.find(taxon_name) else tn = taxon_name end Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id}) end # TODO: This need to be renamed to reflect "simple" association def self.batch_preview(file: nil, ** args) # f = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol) @otus = [] File.open(file).each do |row| name = row.strip next if name.blank? @otus.push(Otu.new(name: row.strip)) end @otus end def self.batch_create(otus: {}, ** args) new_otus = [] begin Otu.transaction do otus.each_key do |k| o = Otu.new(otus[k]) o.save! new_otus.push(o) end end rescue return false end new_otus end # @return [Boolean] # whether or not this otu is coordinate (see coordinate_otus) with this otu def coordinate_with?(otu_id) Otu.coordinate_otus(otu_id).where(otus: {id: id}).any? end # Hernán - this is extremely hacky, I'd like to # map core keys to procs, use yield:, use cached values, # add logic for has_many handling (e.g. identifiers) etc. # ultmately, each key maps to a proc that returns a value # # deprecated for new approach in CollectionObject, AssertedDistribution def dwca_core core = Dwca::GbifProfile::CoreTaxon.new core.nomenclaturalCode = (taxon_name.rank_class.nomenclatural_code.to_s.upcase) core.taxonomicStatus = (taxon_name.unavailable_or_invalid? ? nil : 'accepted') core.nomenclaturalStatus = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking core.scientificName = taxon_name.cached core.scientificNameAuthorship = taxon_name. core.scientificNameID = taxon_name.identifiers.first.identifier core.taxonRank = taxon_name.rank core.namePublishedIn = taxon_name.source.cached core end # TODO: Deprecate for helper method, HTML does not belong here def otu_name if !name.blank? name elsif !taxon_name_id.nil? taxon_name. else nil end end # TODO: move to helper method likely def distribution_geoJSON a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions) c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences) c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area) Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution) end # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination` # @return [Scope] # the max 10 most recently used otus, as `used_on` def self.used_recently(user_id, project_id, used_on = '') t = case used_on when 'AssertedDistribution' AssertedDistribution.arel_table when 'Content' Content.arel_table when 'BiologicalAssociation' BiologicalAssociation.arel_table when 'TaxonDetermination' TaxonDetermination.arel_table else return Otu.none end p = Otu.arel_table # i is a select manager i = case used_on when 'BiologicalAssociation' t.project(t['biological_association_object_id'], t['updated_at']).from(t) .where( t['updated_at'].gt(1.weeks.ago).and( t['biological_association_object_type'].eq('Otu') ) ) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) else t.project(t['otu_id'], t['updated_at']).from(t) .where(t['updated_at'].gt( 1.weeks.ago )) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) end z = i.as('recent_t') case used_on when 'BiologicalAssociation' j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new( z['biological_association_object_id'].eq(p['id']) )) else j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id']))) end Otu.joins(j).pluck(:id).uniq end # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination' # @return [Hash] otus optimized for user selection def self.select_optimized(user_id, project_id, target = nil) r = used_recently(user_id, project_id, target) h = { quick: [], pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a, recent: [] } if target && !r.empty? h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a + Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now) .order('updated_at DESC') .limit(3).to_a ).uniq.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a + Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name} else h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name} end h end protected def check_required_fields if taxon_name_id.blank? && name.blank? errors.add(:taxon_name_id, 'and/or name should be selected') errors.add(:name, 'and/or taxon name should be selected') end end def sv_taxon_name soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil? end def sv_duplicate_otu unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty? m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project" soft_validations.add(:taxon_name_id, m) soft_validations.add(:name, m ) end end end |
#project_id ⇒ Integer
the project ID
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# File 'app/models/otu.rb', line 24 class Otu < ApplicationRecord include Housekeeping include SoftValidation #include Shared::AlternateValues # No alternate values on Name!! include Shared::Citations # TODO: have to think hard about this vs. using Nico's framework include Shared::DataAttributes include Shared::Identifiers include Shared::Notes include Shared::Tags include Shared::Depictions include Shared::Loanable include Shared::Confidences include Shared::Observations include Shared::BiologicalAssociations include Shared::HasPapertrail include Shared::OriginRelationship include Shared::MatrixHooks::Member include Otu::MatrixHooks include Shared::IsData is_origin_for 'Sequence', 'Extract' GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations] belongs_to :taxon_name, inverse_of: :otus has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus has_many :extracts, through: :collection_objects, source: :extracts has_many :sequences, through: :extracts, source: :derived_sequences has_many :collecting_events, -> { distinct }, through: :collection_objects has_many :common_names, dependent: :destroy has_many :collection_profiles, dependent: :restrict_with_error # @proceps dependent: what? has_many :contents, inverse_of: :otu, dependent: :destroy has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area has_many :georeferences, through: :collecting_events has_many :content_topics, through: :contents, source: :topic has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu' has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all has_many :observation_matrices, through: :observation_matrix_rows has_many :observations, inverse_of: :otu, dependent: :restrict_with_error has_many :descriptors, through: :observations scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) } scope :with_name, -> (name) { where(name: name) } # @return Scope def self.alphabetically includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC') end # @param [Integer] otu_id # @param [String] rank_class # @return [Scope] # Otu.joins(:taxon_name).where(taxon_name: q).to_sql def self.self_and_descendants_of(otu_id, rank_class = nil) if o = Otu.joins(:taxon_name).find(otu_id) if rank_class.nil? joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants) else joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class)) end else # no taxon name just return self in scope Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # # All OTUs that are synonymous/same/matching target, for either # historical and pragmatic (i.e. share the same `taxon_name_id`), or # nomenclatural reasons (are synonyms of the taxon name). Includes self. # def self.coordinate_otus(otu_id) begin i = Otu.joins(:taxon_name).find(otu_id) j = i.taxon_name.cached_valid_taxon_name_id o = Otu.arel_table t = TaxonName.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j)) ) Otu.joins(q.join_sources) rescue ActiveRecord::RecordNotFound Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # if the Otu is a child, via synonymy or not, of the taxon name # !! Invalid taxon_name_ids return nothing # !! Taxon names with synonyms return the OTUs of their synonyms def self.descendant_of_taxon_name(taxon_name_id) o = Otu.arel_table t = TaxonName.arel_table h = TaxonNameHierarchy.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id])) .join(h, Arel::Nodes::InnerJoin).on( t[:cached_valid_taxon_name_id].eq(h[:descendant_id])) Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql) end def current_collection_objects collection_objects.where(taxon_determinations: {position: 1}) end validate :check_required_fields soft_validate(:sv_taxon_name, set: :taxon_name) soft_validate(:sv_duplicate_otu, set: :duplicate_otu) accepts_nested_attributes_for :common_names, allow_destroy: true # @return [Otu#id, nil, false] # nil - there is no OTU parent with a valid taxon name possible # false - there is > 1 OTU parent with a valid taxon name possible # id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name # # Note this is used CoLDP export. Do not change without considerations there. def parent_otu_id return nil if taxon_name_id.nil? # TODO: Unify to a single query candidates = TaxonName.joins(:otus, :descendant_hierarchies) .that_is_valid .where.not(id: taxon_name_id) .where(taxon_name_hierarchies: {descendant_id: taxon_name_id}) .order('taxon_name_hierarchies.generations') .limit(1) .pluck(:id) if candidates.size == 1 otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load if otus.size == 1 return otus.first.id elsif otus.count > 1 return false else return nil end else return nil end end # @return [Array] # all bilogical associations this Otu is part of def all_biological_associations # !! If self relationships are ever made possible this needs a DISTINCT clause BiologicalAssociation.find_by_sql( "SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_subject_id = #{self.id} AND biological_associations.biological_association_subject_type = 'Otu' UNION SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_object_id = #{self.id} AND biological_associations.biological_association_object_type = 'Otu' ") end # return [Scope] the Otus bound to that taxon name and its descendants def self.for_taxon_name(taxon_name) if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer) tn = TaxonName.find(taxon_name) else tn = taxon_name end Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id}) end # TODO: This need to be renamed to reflect "simple" association def self.batch_preview(file: nil, ** args) # f = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol) @otus = [] File.open(file).each do |row| name = row.strip next if name.blank? @otus.push(Otu.new(name: row.strip)) end @otus end def self.batch_create(otus: {}, ** args) new_otus = [] begin Otu.transaction do otus.each_key do |k| o = Otu.new(otus[k]) o.save! new_otus.push(o) end end rescue return false end new_otus end # @return [Boolean] # whether or not this otu is coordinate (see coordinate_otus) with this otu def coordinate_with?(otu_id) Otu.coordinate_otus(otu_id).where(otus: {id: id}).any? end # Hernán - this is extremely hacky, I'd like to # map core keys to procs, use yield:, use cached values, # add logic for has_many handling (e.g. identifiers) etc. # ultmately, each key maps to a proc that returns a value # # deprecated for new approach in CollectionObject, AssertedDistribution def dwca_core core = Dwca::GbifProfile::CoreTaxon.new core.nomenclaturalCode = (taxon_name.rank_class.nomenclatural_code.to_s.upcase) core.taxonomicStatus = (taxon_name.unavailable_or_invalid? ? nil : 'accepted') core.nomenclaturalStatus = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking core.scientificName = taxon_name.cached core.scientificNameAuthorship = taxon_name. core.scientificNameID = taxon_name.identifiers.first.identifier core.taxonRank = taxon_name.rank core.namePublishedIn = taxon_name.source.cached core end # TODO: Deprecate for helper method, HTML does not belong here def otu_name if !name.blank? name elsif !taxon_name_id.nil? taxon_name. else nil end end # TODO: move to helper method likely def distribution_geoJSON a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions) c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences) c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area) Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution) end # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination` # @return [Scope] # the max 10 most recently used otus, as `used_on` def self.used_recently(user_id, project_id, used_on = '') t = case used_on when 'AssertedDistribution' AssertedDistribution.arel_table when 'Content' Content.arel_table when 'BiologicalAssociation' BiologicalAssociation.arel_table when 'TaxonDetermination' TaxonDetermination.arel_table else return Otu.none end p = Otu.arel_table # i is a select manager i = case used_on when 'BiologicalAssociation' t.project(t['biological_association_object_id'], t['updated_at']).from(t) .where( t['updated_at'].gt(1.weeks.ago).and( t['biological_association_object_type'].eq('Otu') ) ) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) else t.project(t['otu_id'], t['updated_at']).from(t) .where(t['updated_at'].gt( 1.weeks.ago )) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) end z = i.as('recent_t') case used_on when 'BiologicalAssociation' j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new( z['biological_association_object_id'].eq(p['id']) )) else j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id']))) end Otu.joins(j).pluck(:id).uniq end # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination' # @return [Hash] otus optimized for user selection def self.select_optimized(user_id, project_id, target = nil) r = used_recently(user_id, project_id, target) h = { quick: [], pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a, recent: [] } if target && !r.empty? h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a + Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now) .order('updated_at DESC') .limit(3).to_a ).uniq.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a + Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name} else h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name} end h end protected def check_required_fields if taxon_name_id.blank? && name.blank? errors.add(:taxon_name_id, 'and/or name should be selected') errors.add(:name, 'and/or taxon name should be selected') end end def sv_taxon_name soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil? end def sv_duplicate_otu unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty? m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project" soft_validations.add(:taxon_name_id, m) soft_validations.add(:name, m ) end end end |
#taxon_name_id ⇒ Integer
The id of the nomenclatural name for this OTU. The presence of a nomenclatural name carries no biological meaning, it is simply a means to organize concepts within a nomenclatural system.
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# File 'app/models/otu.rb', line 24 class Otu < ApplicationRecord include Housekeeping include SoftValidation #include Shared::AlternateValues # No alternate values on Name!! include Shared::Citations # TODO: have to think hard about this vs. using Nico's framework include Shared::DataAttributes include Shared::Identifiers include Shared::Notes include Shared::Tags include Shared::Depictions include Shared::Loanable include Shared::Confidences include Shared::Observations include Shared::BiologicalAssociations include Shared::HasPapertrail include Shared::OriginRelationship include Shared::MatrixHooks::Member include Otu::MatrixHooks include Shared::IsData is_origin_for 'Sequence', 'Extract' GRAPH_ENTRY_POINTS = [:asserted_distributions, :biological_associations, :common_names, :contents, :data_attributes, :taxon_determinations] belongs_to :taxon_name, inverse_of: :otus has_many :asserted_distributions, inverse_of: :otu, dependent: :restrict_with_error has_many :biological_associations, as: :biological_association_subject, inverse_of: :biological_association_subject, dependent: :restrict_with_error has_many :related_biological_associations, as: :biological_association_object, inverse_of: :biological_association_object, class_name: 'BiologicalAssociation', dependent: :restrict_with_error has_many :taxon_determinations, inverse_of: :otu, dependent: :destroy # TODO: change has_many :collection_objects, through: :taxon_determinations, source: :biological_collection_object, inverse_of: :otus has_many :extracts, through: :collection_objects, source: :extracts has_many :sequences, through: :extracts, source: :derived_sequences has_many :collecting_events, -> { distinct }, through: :collection_objects has_many :common_names, dependent: :destroy has_many :collection_profiles, dependent: :restrict_with_error # @proceps dependent: what? has_many :contents, inverse_of: :otu, dependent: :destroy has_many :geographic_areas_from_asserted_distributions, through: :asserted_distributions, source: :geographic_area has_many :geographic_areas_from_collecting_events, through: :collecting_events, source: :geographic_area has_many :georeferences, through: :collecting_events has_many :content_topics, through: :contents, source: :topic has_many :observation_matrix_row_items, inverse_of: :otu, dependent: :delete_all, class_name: 'ObservationMatrixRowItem::Single::Otu' has_many :observation_matrix_rows, inverse_of: :collection_object, dependent: :delete_all has_many :observation_matrices, through: :observation_matrix_rows has_many :observations, inverse_of: :otu, dependent: :restrict_with_error has_many :descriptors, through: :observations scope :with_taxon_name_id, -> (taxon_name_id) { where(taxon_name_id: taxon_name_id) } scope :with_name, -> (name) { where(name: name) } # @return Scope def self.alphabetically includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC') end # @param [Integer] otu_id # @param [String] rank_class # @return [Scope] # Otu.joins(:taxon_name).where(taxon_name: q).to_sql def self.self_and_descendants_of(otu_id, rank_class = nil) if o = Otu.joins(:taxon_name).find(otu_id) if rank_class.nil? joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants) else joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class)) end else # no taxon name just return self in scope Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # # All OTUs that are synonymous/same/matching target, for either # historical and pragmatic (i.e. share the same `taxon_name_id`), or # nomenclatural reasons (are synonyms of the taxon name). Includes self. # def self.coordinate_otus(otu_id) begin i = Otu.joins(:taxon_name).find(otu_id) j = i.taxon_name.cached_valid_taxon_name_id o = Otu.arel_table t = TaxonName.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j)) ) Otu.joins(q.join_sources) rescue ActiveRecord::RecordNotFound Otu.where(id: otu_id) end end # @return [Otu::ActiveRecordRelation] # if the Otu is a child, via synonymy or not, of the taxon name # !! Invalid taxon_name_ids return nothing # !! Taxon names with synonyms return the OTUs of their synonyms def self.descendant_of_taxon_name(taxon_name_id) o = Otu.arel_table t = TaxonName.arel_table h = TaxonNameHierarchy.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id])) .join(h, Arel::Nodes::InnerJoin).on( t[:cached_valid_taxon_name_id].eq(h[:descendant_id])) Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql) end def current_collection_objects collection_objects.where(taxon_determinations: {position: 1}) end validate :check_required_fields soft_validate(:sv_taxon_name, set: :taxon_name) soft_validate(:sv_duplicate_otu, set: :duplicate_otu) accepts_nested_attributes_for :common_names, allow_destroy: true # @return [Otu#id, nil, false] # nil - there is no OTU parent with a valid taxon name possible # false - there is > 1 OTU parent with a valid taxon name possible # id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name # # Note this is used CoLDP export. Do not change without considerations there. def parent_otu_id return nil if taxon_name_id.nil? # TODO: Unify to a single query candidates = TaxonName.joins(:otus, :descendant_hierarchies) .that_is_valid .where.not(id: taxon_name_id) .where(taxon_name_hierarchies: {descendant_id: taxon_name_id}) .order('taxon_name_hierarchies.generations') .limit(1) .pluck(:id) if candidates.size == 1 otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load if otus.size == 1 return otus.first.id elsif otus.count > 1 return false else return nil end else return nil end end # @return [Array] # all bilogical associations this Otu is part of def all_biological_associations # !! If self relationships are ever made possible this needs a DISTINCT clause BiologicalAssociation.find_by_sql( "SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_subject_id = #{self.id} AND biological_associations.biological_association_subject_type = 'Otu' UNION SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_object_id = #{self.id} AND biological_associations.biological_association_object_type = 'Otu' ") end # return [Scope] the Otus bound to that taxon name and its descendants def self.for_taxon_name(taxon_name) if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer) tn = TaxonName.find(taxon_name) else tn = taxon_name end Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id}) end # TODO: This need to be renamed to reflect "simple" association def self.batch_preview(file: nil, ** args) # f = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol) @otus = [] File.open(file).each do |row| name = row.strip next if name.blank? @otus.push(Otu.new(name: row.strip)) end @otus end def self.batch_create(otus: {}, ** args) new_otus = [] begin Otu.transaction do otus.each_key do |k| o = Otu.new(otus[k]) o.save! new_otus.push(o) end end rescue return false end new_otus end # @return [Boolean] # whether or not this otu is coordinate (see coordinate_otus) with this otu def coordinate_with?(otu_id) Otu.coordinate_otus(otu_id).where(otus: {id: id}).any? end # Hernán - this is extremely hacky, I'd like to # map core keys to procs, use yield:, use cached values, # add logic for has_many handling (e.g. identifiers) etc. # ultmately, each key maps to a proc that returns a value # # deprecated for new approach in CollectionObject, AssertedDistribution def dwca_core core = Dwca::GbifProfile::CoreTaxon.new core.nomenclaturalCode = (taxon_name.rank_class.nomenclatural_code.to_s.upcase) core.taxonomicStatus = (taxon_name.unavailable_or_invalid? ? nil : 'accepted') core.nomenclaturalStatus = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking core.scientificName = taxon_name.cached core.scientificNameAuthorship = taxon_name. core.scientificNameID = taxon_name.identifiers.first.identifier core.taxonRank = taxon_name.rank core.namePublishedIn = taxon_name.source.cached core end # TODO: Deprecate for helper method, HTML does not belong here def otu_name if !name.blank? name elsif !taxon_name_id.nil? taxon_name. else nil end end # TODO: move to helper method likely def distribution_geoJSON a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions) c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences) c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area) Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution) end # @param used_on [String] required, one of `AssertedDistribution`, `Content`, `BiologicalAssociation`, `TaxonDetermination` # @return [Scope] # the max 10 most recently used otus, as `used_on` def self.used_recently(user_id, project_id, used_on = '') t = case used_on when 'AssertedDistribution' AssertedDistribution.arel_table when 'Content' Content.arel_table when 'BiologicalAssociation' BiologicalAssociation.arel_table when 'TaxonDetermination' TaxonDetermination.arel_table else return Otu.none end p = Otu.arel_table # i is a select manager i = case used_on when 'BiologicalAssociation' t.project(t['biological_association_object_id'], t['updated_at']).from(t) .where( t['updated_at'].gt(1.weeks.ago).and( t['biological_association_object_type'].eq('Otu') ) ) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) else t.project(t['otu_id'], t['updated_at']).from(t) .where(t['updated_at'].gt( 1.weeks.ago )) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) end z = i.as('recent_t') case used_on when 'BiologicalAssociation' j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new( z['biological_association_object_id'].eq(p['id']) )) else j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id']))) end Otu.joins(j).pluck(:id).uniq end # @params target [String] required, one of nil, `AssertedDistribution`, `Content`, `BiologicalAssociation`, 'TaxonDetermination' # @return [Hash] otus optimized for user selection def self.select_optimized(user_id, project_id, target = nil) r = used_recently(user_id, project_id, target) h = { quick: [], pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a, recent: [] } if target && !r.empty? h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a + Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now) .order('updated_at DESC') .limit(3).to_a ).uniq.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a + Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name} else h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name} end h end protected def check_required_fields if taxon_name_id.blank? && name.blank? errors.add(:taxon_name_id, 'and/or name should be selected') errors.add(:name, 'and/or taxon name should be selected') end end def sv_taxon_name soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil? end def sv_duplicate_otu unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty? m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project" soft_validations.add(:taxon_name_id, m) soft_validations.add(:name, m ) end end end |
Class Method Details
.alphabetically ⇒ Object
Returns Scope.
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# File 'app/models/otu.rb', line 84 def self.alphabetically includes(:taxon_name).select('otus.*, taxon_names.cached').references(:taxon_names).order('taxon_names.cached ASC') end |
.batch_create(otus: {}, **args) ⇒ Object
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# File 'app/models/otu.rb', line 226 def self.batch_create(otus: {}, ** args) new_otus = [] begin Otu.transaction do otus.each_key do |k| o = Otu.new(otus[k]) o.save! new_otus.push(o) end end rescue return false end new_otus end |
.batch_preview(file: nil, **args) ⇒ Object
TODO: This need to be renamed to reflect “simple” association
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# File 'app/models/otu.rb', line 215 def self.batch_preview(file: nil, ** args) # f = CSV.read(file, headers: true, col_sep: "\t", skip_blanks: true, header_converters: :symbol) @otus = [] File.open(file).each do |row| name = row.strip next if name.blank? @otus.push(Otu.new(name: row.strip)) end @otus end |
.coordinate_otus(otu_id) ⇒ Otu::ActiveRecordRelation
All OTUs that are synonymous/same/matching target, for either
historical and pragmatic (i.e. share the same `taxon_name_id`), or
nomenclatural reasons (are synonyms of the taxon name). Includes self.
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# File 'app/models/otu.rb', line 110 def self.coordinate_otus(otu_id) begin i = Otu.joins(:taxon_name).find(otu_id) j = i.taxon_name.cached_valid_taxon_name_id o = Otu.arel_table t = TaxonName.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id] ).and(t[:cached_valid_taxon_name_id].eq(j)) ) Otu.joins(q.join_sources) rescue ActiveRecord::RecordNotFound Otu.where(id: otu_id) end end |
.descendant_of_taxon_name(taxon_name_id) ⇒ Otu::ActiveRecordRelation
Returns if the Otu is a child, via synonymy or not, of the taxon name !! Invalid taxon_name_ids return nothing !! Taxon names with synonyms return the OTUs of their synonyms.
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# File 'app/models/otu.rb', line 131 def self.descendant_of_taxon_name(taxon_name_id) o = Otu.arel_table t = TaxonName.arel_table h = TaxonNameHierarchy.arel_table q = o.join(t, Arel::Nodes::InnerJoin).on( o[:taxon_name_id].eq( t[:id])) .join(h, Arel::Nodes::InnerJoin).on( t[:cached_valid_taxon_name_id].eq(h[:descendant_id])) Otu.joins(q.join_sources).where(h[:ancestor_id].eq(taxon_name_id).to_sql) end |
.for_taxon_name(taxon_name) ⇒ Object
return [Scope] the Otus bound to that taxon name and its descendants
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# File 'app/models/otu.rb', line 205 def self.for_taxon_name(taxon_name) if taxon_name.kind_of?(String) || taxon_name.kind_of?(Integer) tn = TaxonName.find(taxon_name) else tn = taxon_name end Otu.joins(taxon_name: [:ancestor_hierarchies]).where(taxon_name_hierarchies: {ancestor_id: tn.id}) end |
.select_optimized(user_id, project_id, target = nil) ⇒ Hash
Returns otus optimized for user selection.
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# File 'app/models/otu.rb', line 342 def self.select_optimized(user_id, project_id, target = nil) r = used_recently(user_id, project_id, target) h = { quick: [], pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a, recent: [] } if target && !r.empty? h[:recent] = (Otu.where('"otus"."id" IN (?)', r.first(10) ).to_a + Otu.where(project_id: project_id, created_by_id: user_id, created_at: 3.hours.ago..Time.now) .order('updated_at DESC') .limit(3).to_a ).uniq.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = (Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a + Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name} else h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name} h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name} end h end |
.self_and_descendants_of(otu_id, rank_class = nil) ⇒ Scope
Returns Otu.joins(:taxon_name).where(taxon_name: q).to_sql.
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# File 'app/models/otu.rb', line 92 def self.self_and_descendants_of(otu_id, rank_class = nil) if o = Otu.joins(:taxon_name).find(otu_id) if rank_class.nil? joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants) else joins(:taxon_name).where(taxon_name: o.taxon_name.self_and_descendants.where( rank_class: rank_class)) end else # no taxon name just return self in scope Otu.where(id: otu_id) end end |
.used_recently(user_id, project_id, used_on = '') ⇒ Scope
Returns the max 10 most recently used otus, as `used_on`.
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# File 'app/models/otu.rb', line 290 def self.used_recently(user_id, project_id, used_on = '') t = case used_on when 'AssertedDistribution' AssertedDistribution.arel_table when 'Content' Content.arel_table when 'BiologicalAssociation' BiologicalAssociation.arel_table when 'TaxonDetermination' TaxonDetermination.arel_table else return Otu.none end p = Otu.arel_table # i is a select manager i = case used_on when 'BiologicalAssociation' t.project(t['biological_association_object_id'], t['updated_at']).from(t) .where( t['updated_at'].gt(1.weeks.ago).and( t['biological_association_object_type'].eq('Otu') ) ) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) else t.project(t['otu_id'], t['updated_at']).from(t) .where(t['updated_at'].gt( 1.weeks.ago )) .where(t['created_by_id'].eq(user_id)) .where(t['project_id'].eq(project_id)) .order(t['updated_at'].desc) end z = i.as('recent_t') case used_on when 'BiologicalAssociation' j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new( z['biological_association_object_id'].eq(p['id']) )) else j = Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['otu_id'].eq(p['id']))) end Otu.joins(j).pluck(:id).uniq end |
Instance Method Details
#all_biological_associations ⇒ Array
Returns all bilogical associations this Otu is part of.
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# File 'app/models/otu.rb', line 190 def all_biological_associations # !! If self relationships are ever made possible this needs a DISTINCT clause BiologicalAssociation.find_by_sql( "SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_subject_id = #{self.id} AND biological_associations.biological_association_subject_type = 'Otu' UNION SELECT biological_associations.* FROM biological_associations WHERE biological_associations.biological_association_object_id = #{self.id} AND biological_associations.biological_association_object_type = 'Otu' ") end |
#check_required_fields ⇒ Object (protected)
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# File 'app/models/otu.rb', line 368 def check_required_fields if taxon_name_id.blank? && name.blank? errors.add(:taxon_name_id, 'and/or name should be selected') errors.add(:name, 'and/or taxon name should be selected') end end |
#coordinate_with?(otu_id) ⇒ Boolean
Returns whether or not this otu is coordinate (see coordinate_otus) with this otu.
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# File 'app/models/otu.rb', line 244 def coordinate_with?(otu_id) Otu.coordinate_otus(otu_id).where(otus: {id: id}).any? end |
#current_collection_objects ⇒ Object
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# File 'app/models/otu.rb', line 144 def current_collection_objects collection_objects.where(taxon_determinations: {position: 1}) end |
#distribution_geoJSON ⇒ Object
TODO: move to helper method likely
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# File 'app/models/otu.rb', line 280 def distribution_geoJSON a_ds = Gis::GeoJSON.feature_collection(geographic_areas_from_asserted_distributions, :asserted_distributions) c_os = Gis::GeoJSON.feature_collection(collecting_events, :collecting_events_georeferences) c_es = Gis::GeoJSON.feature_collection(geographic_areas_from_collecting_events, :collecting_events_geographic_area) Gis::GeoJSON.aggregation([a_ds, c_os, c_es], :distribution) end |
#dwca_core ⇒ Object
Hernán - this is extremely hacky, I'd like to map core keys to procs, use yield:, use cached values, add logic for has_many handling (e.g. identifiers) etc. ultmately, each key maps to a proc that returns a value
deprecated for new approach in CollectionObject, AssertedDistribution
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# File 'app/models/otu.rb', line 254 def dwca_core core = Dwca::GbifProfile::CoreTaxon.new core.nomenclaturalCode = (taxon_name.rank_class.nomenclatural_code.to_s.upcase) core.taxonomicStatus = (taxon_name.unavailable_or_invalid? ? nil : 'accepted') core.nomenclaturalStatus = (taxon_name.classification_invalid_or_unavailable? ? nil : 'available') # needs tweaking core.scientificName = taxon_name.cached core.scientificNameAuthorship = taxon_name. core.scientificNameID = taxon_name.identifiers.first.identifier core.taxonRank = taxon_name.rank core.namePublishedIn = taxon_name.source.cached core end |
#otu_name ⇒ Object
TODO: Deprecate for helper method, HTML does not belong here
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# File 'app/models/otu.rb', line 269 def otu_name if !name.blank? name elsif !taxon_name_id.nil? taxon_name. else nil end end |
#parent_otu_id ⇒ Otu#id, ...
Returns nil - there is no OTU parent with a valid taxon name possible false - there is > 1 OTU parent with a valid taxon name possible id - the (unambiguous) id of the nearest parent OTU attached to a valid taoxn name
Note this is used CoLDP export. Do not change without considerations there.
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# File 'app/models/otu.rb', line 161 def parent_otu_id return nil if taxon_name_id.nil? # TODO: Unify to a single query candidates = TaxonName.joins(:otus, :descendant_hierarchies) .that_is_valid .where.not(id: taxon_name_id) .where(taxon_name_hierarchies: {descendant_id: taxon_name_id}) .order('taxon_name_hierarchies.generations') .limit(1) .pluck(:id) if candidates.size == 1 otus = Otu.where(taxon_name_id: candidates.first).limit(1).limit(2).load if otus.size == 1 return otus.first.id elsif otus.count > 1 return false else return nil end else return nil end end |
#sv_duplicate_otu ⇒ Object (protected)
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# File 'app/models/otu.rb', line 379 def sv_duplicate_otu unless Otu.with_taxon_name_id(taxon_name_id).with_name(name).not_self(self).with_project_id(project_id).empty? m = "Another OTU with an identical nomenclature (taxon name) and name exists in this project" soft_validations.add(:taxon_name_id, m) soft_validations.add(:name, m ) end end |
#sv_taxon_name ⇒ Object (protected)
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# File 'app/models/otu.rb', line 375 def sv_taxon_name soft_validations.add(:taxon_name_id, 'Nomenclature (taxon name) is not assigned') if taxon_name_id.nil? end |