Class: Extract

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::AutoUuid, Shared::Citations, Shared::Confidences, Shared::Containable, Shared::DataAttributes, Shared::Identifiers, Shared::IsData, Shared::Observations, Shared::OriginRelationship, Shared::ProtocolRelationships, Shared::Tags, SoftValidation
Defined in:
app/models/extract.rb

Overview

An Extract is the quantified physical entity that originated from a CollectionObject. Extracts are linked to their origin through an OriginRelationship.

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::AutoUuid

#create_object_uuid, #generate_uuid_if_required

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 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::Tags

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

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 Shared::Confidences

#reject_confidences

Methods included from Shared::Containable

#contain, #containable?, #contained?, #contained_by?, #contained_siblings, #enclosing_containers, #put_in_container

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::ProtocolRelationships

#protocolled?, #reject_protocols

Methods included from Shared::Identifiers

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

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#day_made ⇒ Integer

Returns 2 digit day the extract originated.

Returns:

  • (Integer) —

    2 digit day the extract originated



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# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::Confidences
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Observations
  include Shared::Tags
  include SoftValidation
  include Shared::IsData
  include Shared::AutoUuid

  # TODO: make loanable
  # TODO: auto-UUID

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu', 'CollectionObject', 'FieldOccurrence'

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true, inverse_of: :role_object
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true

  # Upstream - aliases of `origin_otus` and `origin_collection_objects` TODO remove
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm - aliases of `derived_*`, TODO: remove
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'

  attr_accessor :is_made_now

  # TODO: Unify in concern, with CO too
  # Identifier delegations
  # .catalog_number_cached
  delegate :cached, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true
  # .catalog_number_namespace
  delegate :namespace, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true

  before_validation :set_made, if: -> {is_made_now}

  validates :year_made, date_year: { min_year: 1757, max_year: -> {Time.now.year} }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # @return Array
  #   all inferred or asserted OTUs that this OTU came from
  def referenced_otus
    [
      [otus],
      [collection_objects.collect{|o| o.current_otu} ]
    ].flatten.compact.uniq
  end

  # TODO: Unify with CollectionObject in concern
  # @return [Identifier::Local::CatalogNumber, nil]
  #   the first (position) catalog number for this collection object, either on specimen, or container
  def preferred_catalog_number
    if i = Identifier::Local::CatalogNumber.where(identifier_object: self).order(:position).first
      i
    else
      if container
        container.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'}).order(:position).first
      else
        nil
      end
    end
  end

  # In anticipation of DwC handling
  def dwc_catalog_number
    catalog_number_cached
  end

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  # @param used_on [String] required, one of `Protocol`, `OriginRelationship`
  # @return [Scope]
  #    the max 10 most recently used collection_objects, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    return [] if used_on != 'TaxonDetermination' && used_on != 'BiologicalAssociation'
    t = case used_on
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        end

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject')
              )
            )
              .where(t['updated_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['taxon_determination_object_id'], t['taxon_determination_object_type'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.week.ago ))
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    # z is a table alias
    z = i.as('recent_t')

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          # TODO fix biological_collection_object_id transition scoping
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['taxon_determination_object_id'].eq(p['id'])))
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @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: Extract.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = Extract.where('"extracts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
          Extract.where('"extracts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = Extract.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

end

#is_made_now ⇒ Object

Returns the value of attribute is_made_now.



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# File 'app/models/extract.rb', line 54

def is_made_now
  @is_made_now
end

#month_made ⇒ Integer

Returns 2 digit month the extract originated.

Returns:

  • (Integer) —

    2 digit month the extract originated



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# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::Confidences
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Observations
  include Shared::Tags
  include SoftValidation
  include Shared::IsData
  include Shared::AutoUuid

  # TODO: make loanable
  # TODO: auto-UUID

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu', 'CollectionObject', 'FieldOccurrence'

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true, inverse_of: :role_object
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true

  # Upstream - aliases of `origin_otus` and `origin_collection_objects` TODO remove
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm - aliases of `derived_*`, TODO: remove
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'

  attr_accessor :is_made_now

  # TODO: Unify in concern, with CO too
  # Identifier delegations
  # .catalog_number_cached
  delegate :cached, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true
  # .catalog_number_namespace
  delegate :namespace, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true

  before_validation :set_made, if: -> {is_made_now}

  validates :year_made, date_year: { min_year: 1757, max_year: -> {Time.now.year} }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # @return Array
  #   all inferred or asserted OTUs that this OTU came from
  def referenced_otus
    [
      [otus],
      [collection_objects.collect{|o| o.current_otu} ]
    ].flatten.compact.uniq
  end

  # TODO: Unify with CollectionObject in concern
  # @return [Identifier::Local::CatalogNumber, nil]
  #   the first (position) catalog number for this collection object, either on specimen, or container
  def preferred_catalog_number
    if i = Identifier::Local::CatalogNumber.where(identifier_object: self).order(:position).first
      i
    else
      if container
        container.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'}).order(:position).first
      else
        nil
      end
    end
  end

  # In anticipation of DwC handling
  def dwc_catalog_number
    catalog_number_cached
  end

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  # @param used_on [String] required, one of `Protocol`, `OriginRelationship`
  # @return [Scope]
  #    the max 10 most recently used collection_objects, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    return [] if used_on != 'TaxonDetermination' && used_on != 'BiologicalAssociation'
    t = case used_on
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        end

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject')
              )
            )
              .where(t['updated_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['taxon_determination_object_id'], t['taxon_determination_object_type'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.week.ago ))
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    # z is a table alias
    z = i.as('recent_t')

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          # TODO fix biological_collection_object_id transition scoping
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['taxon_determination_object_id'].eq(p['id'])))
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @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: Extract.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = Extract.where('"extracts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
          Extract.where('"extracts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = Extract.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

end

#verbatim_anatomical_origin ⇒ String

Returns proxy for a OriginRelationship to an AnatomicalClass.

Returns:

  • (String) —

    proxy for a OriginRelationship to an AnatomicalClass



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# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::Confidences
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Observations
  include Shared::Tags
  include SoftValidation
  include Shared::IsData
  include Shared::AutoUuid

  # TODO: make loanable
  # TODO: auto-UUID

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu', 'CollectionObject', 'FieldOccurrence'

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true, inverse_of: :role_object
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true

  # Upstream - aliases of `origin_otus` and `origin_collection_objects` TODO remove
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm - aliases of `derived_*`, TODO: remove
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'

  attr_accessor :is_made_now

  # TODO: Unify in concern, with CO too
  # Identifier delegations
  # .catalog_number_cached
  delegate :cached, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true
  # .catalog_number_namespace
  delegate :namespace, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true

  before_validation :set_made, if: -> {is_made_now}

  validates :year_made, date_year: { min_year: 1757, max_year: -> {Time.now.year} }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # @return Array
  #   all inferred or asserted OTUs that this OTU came from
  def referenced_otus
    [
      [otus],
      [collection_objects.collect{|o| o.current_otu} ]
    ].flatten.compact.uniq
  end

  # TODO: Unify with CollectionObject in concern
  # @return [Identifier::Local::CatalogNumber, nil]
  #   the first (position) catalog number for this collection object, either on specimen, or container
  def preferred_catalog_number
    if i = Identifier::Local::CatalogNumber.where(identifier_object: self).order(:position).first
      i
    else
      if container
        container.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'}).order(:position).first
      else
        nil
      end
    end
  end

  # In anticipation of DwC handling
  def dwc_catalog_number
    catalog_number_cached
  end

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  # @param used_on [String] required, one of `Protocol`, `OriginRelationship`
  # @return [Scope]
  #    the max 10 most recently used collection_objects, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    return [] if used_on != 'TaxonDetermination' && used_on != 'BiologicalAssociation'
    t = case used_on
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        end

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject')
              )
            )
              .where(t['updated_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['taxon_determination_object_id'], t['taxon_determination_object_type'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.week.ago ))
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    # z is a table alias
    z = i.as('recent_t')

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          # TODO fix biological_collection_object_id transition scoping
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['taxon_determination_object_id'].eq(p['id'])))
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @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: Extract.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = Extract.where('"extracts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
          Extract.where('"extracts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = Extract.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

end

#year_made ⇒ Integer

Returns 4 digit year the extract originated.

Returns:

  • (Integer) —

    4 digit year the extract originated



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# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::Confidences
  include Shared::Citations
  include Shared::DataAttributes
  include Shared::Observations
  include Shared::Tags
  include SoftValidation
  include Shared::IsData
  include Shared::AutoUuid

  # TODO: make loanable
  # TODO: auto-UUID

  is_origin_for 'Extract', 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Otu', 'CollectionObject', 'FieldOccurrence'

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true, inverse_of: :role_object
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true

  # Upstream - aliases of `origin_otus` and `origin_collection_objects` TODO remove
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm - aliases of `derived_*`, TODO: remove
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'

  attr_accessor :is_made_now

  # TODO: Unify in concern, with CO too
  # Identifier delegations
  # .catalog_number_cached
  delegate :cached, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true
  # .catalog_number_namespace
  delegate :namespace, to: :preferred_catalog_number, prefix: :catalog_number, allow_nil: true

  before_validation :set_made, if: -> {is_made_now}

  validates :year_made, date_year: { min_year: 1757, max_year: -> {Time.now.year} }
  validates :month_made, date_month: true
  validates :day_made, date_day: {year_sym: :year_made, month_sym: :month_made}, unless: -> {year_made.nil? || month_made.nil?}

  # @return Array
  #   all inferred or asserted OTUs that this OTU came from
  def referenced_otus
    [
      [otus],
      [collection_objects.collect{|o| o.current_otu} ]
    ].flatten.compact.uniq
  end

  # TODO: Unify with CollectionObject in concern
  # @return [Identifier::Local::CatalogNumber, nil]
  #   the first (position) catalog number for this collection object, either on specimen, or container
  def preferred_catalog_number
    if i = Identifier::Local::CatalogNumber.where(identifier_object: self).order(:position).first
      i
    else
      if container
        container.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'}).order(:position).first
      else
        nil
      end
    end
  end

  # In anticipation of DwC handling
  def dwc_catalog_number
    catalog_number_cached
  end

  protected

  def set_made
    write_attribute(:year_made, Time.now.year)
    write_attribute(:month_made, Time.now.month)
    write_attribute(:day_made, Time.now.day)
  end

  # @param used_on [String] required, one of `Protocol`, `OriginRelationship`
  # @return [Scope]
  #    the max 10 most recently used collection_objects, as `used_on`
  def self.used_recently(user_id, project_id, used_on = '')
    return [] if used_on != 'TaxonDetermination' && used_on != 'BiologicalAssociation'
    t = case used_on
        when 'TaxonDetermination'
          TaxonDetermination.arel_table
        when 'BiologicalAssociation'
          BiologicalAssociation.arel_table
        end

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.week.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject')
              )
            )
              .where(t['updated_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['taxon_determination_object_id'], t['taxon_determination_object_type'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.week.ago ))
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

    # z is a table alias
    z = i.as('recent_t')

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          # TODO fix biological_collection_object_id transition scoping
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['taxon_determination_object_id'].eq(p['id'])))
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @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: Extract.pinned_by(user_id).where(project_id:).to_a,
      recent: []
    }

    if target && !r.empty?
      n = target.tableize.to_sym
      h[:recent] = Extract.where('"extracts"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
          Extract.where('"extracts"."id" IN (?)', r.first(4) ).to_a).uniq
    else
      h[:recent] = Extract.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
      h[:quick] = Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
    end

    h
  end

end

Class Method Details

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

Returns otus optimized for user selection.

Returns:

  • (Hash) —

    otus optimized for user selection



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# File 'app/models/extract.rb', line 158

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

  if target && !r.empty?
    n = target.tableize.to_sym
    h[:recent] = Extract.where('"extracts"."id" IN (?)', r.first(10) ).to_a
    h[:quick] = (Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a  +
        Extract.where('"extracts"."id" IN (?)', r.first(4) ).to_a).uniq
  else
    h[:recent] = Extract.where(project_id:, updated_by_id: user_id).order('updated_at DESC').limit(10).to_a
    h[:quick] = Extract.pinned_by(user_id).pinboard_inserted.where(project_id:).to_a
  end

  h
end

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

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

Parameters:

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

    required, one of ‘Protocol`, `OriginRelationship`

Returns:

  • (Scope) —

    the max 10 most recently used collection_objects, as ‘used_on`



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# File 'app/models/extract.rb', line 109

def self.used_recently(user_id, project_id, used_on = '')
  return [] if used_on != 'TaxonDetermination' && used_on != 'BiologicalAssociation'
  t = case used_on
      when 'TaxonDetermination'
        TaxonDetermination.arel_table
      when 'BiologicalAssociation'
        BiologicalAssociation.arel_table
      end

  p = CollectionObject.arel_table

  # i is a select manager
  i = case used_on
      when 'BiologicalAssociation'
        t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
          .where(
            t['updated_at'].gt(1.week.ago).and(
              t['biological_association_subject_type'].eq('CollectionObject')
            )
          )
            .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      else
        t.project(t['taxon_determination_object_id'], t['taxon_determination_object_type'], t['updated_at']).from(t)
          .where(t['updated_at'].gt( 1.week.ago ))
          .where(t['updated_by_id'].eq(user_id))
          .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      end

  # z is a table alias
  z = i.as('recent_t')

  j = case used_on
      when 'BiologicalAssociation'
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
          z['biological_association_subject_id'].eq(p['id'])
        ))
      else
        # TODO fix biological_collection_object_id transition scoping
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['taxon_determination_object_id'].eq(p['id'])))
      end

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

Instance Method Details

#dwc_catalog_number ⇒ Object

In anticipation of DwC handling



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# File 'app/models/extract.rb', line 94

def dwc_catalog_number
  catalog_number_cached
end

#preferred_catalog_number ⇒ Identifier::Local::CatalogNumber?

TODO: Unify with CollectionObject in concern

Returns:



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# File 'app/models/extract.rb', line 81

def preferred_catalog_number
  if i = Identifier::Local::CatalogNumber.where(identifier_object: self).order(:position).first
    i
  else
    if container
      container.identifiers.where(identifiers: {type: 'Identifier::Local::CatalogNumber'}).order(:position).first
    else
      nil
    end
  end
end

#referenced_otus ⇒ Object

Returns Array all inferred or asserted OTUs that this OTU came from.

Returns:

  • Array all inferred or asserted OTUs that this OTU came from



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# File 'app/models/extract.rb', line 71

def referenced_otus
  [
    [otus],
    [collection_objects.collect{|o| o.current_otu} ]
  ].flatten.compact.uniq
end

#set_made ⇒ Object (protected) 



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# File 'app/models/extract.rb', line 100

def set_made
  write_attribute(:year_made, Time.now.year)
  write_attribute(:month_made, Time.now.month)
  write_attribute(:day_made, Time.now.day)
end