Class: Sequence

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::AlternateValues, Shared::Confidences, Shared::DataAttributes, Shared::Documentation, Shared::HasPapertrail, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::OriginRelationship, Shared::ProtocolRelationships, Shared::Tags
Defined in:
app/models/sequence.rb

Overview

A DNA, RNA, or Amino Acid, as defined by a string of letters. All other attributes are stored in related tables, the overal model is basically a graph with nodes having attributes.

Constant Summary collapse

ALTERNATE_VALUES_FOR = 
[:name].freeze

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

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

Methods included from Shared::HasPapertrail

#attribute_updated, #attribute_updater

Methods included from Shared::Tags

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

Methods included from Shared::ProtocolRelationships

#protocolled?, #reject_protocols

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Identifiers

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

Methods included from Shared::Documentation

#document_array=, #documented?, #reject_documentation, #reject_documents

Methods included from Shared::Confidences

#reject_confidences

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::AlternateValues

#all_values_for, #alternate_valued?

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#describe_with ⇒ Object

Pass a Gene::Descriptor instance to clone that description to this sequence



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# File 'app/models/sequence.rb', line 44

def describe_with
  @describe_with
end

#name ⇒ String

Returns the asserted name for this sequence, typically the target gene name like “CO1”. Important! The preferred mechanism for assinging this type of label to a sequence is assigning pertinent metadata (relationships to other sequences) and then inferrning that those sequences with particular metadata have a specific gene name (Descriptor::Gene#name).

Returns:

  • (String) —

    the asserted name for this sequence, typically the target gene name like “CO1”. Important! The preferred mechanism for assinging this type of label to a sequence is assigning pertinent metadata (relationships to other sequences) and then inferrning that those sequences with particular metadata have a specific gene name (Descriptor::Gene#name).



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# File 'app/models/sequence.rb', line 22

class Sequence < ApplicationRecord

  include Housekeeping

  include Shared::AlternateValues
  include Shared::DataAttributes
  include Shared::Confidences
  include Shared::Documentation
  include Shared::Identifiers
  include Shared::Notes
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::HasPapertrail
  include Shared::IsData

  is_origin_for 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Sequence'

  ALTERNATE_VALUES_FOR = [:name].freeze

  # Pass a Gene::Descriptor instance to clone that description to this sequence
  attr_accessor :describe_with

  has_many :sequence_relationships, foreign_key: :subject_sequence_id, inverse_of: :subject_sequence # this sequence describes others
  has_many :sequences, through: :sequence_relationships, source: :object_sequence

  has_many :related_sequence_relationships, class_name: 'SequenceRelationship', foreign_key: :object_sequence_id, inverse_of: :object_sequence # attributes of this sequence
  has_many :related_sequences, through: :related_sequence_relationships, source: :subject_sequence
  has_many :gene_attributes, inverse_of: :sequence

  # has_many :descriptors, through: :gene_attributes, inverse_of: :sequences, as: 'Descriptor::Gene'

  before_validation :build_relationships, if: -> {describe_with.present?}
  before_validation :normalize_sequence_type

  SequenceRelationship.descendants.each do |d|
    t = d.name.demodulize.tableize.singularize
    relationships = "#{t}_relationships".to_sym
    sequences = "#{t}_sequences".to_sym

    has_many relationships, class_name: d.name.to_s, foreign_key: :object_sequence_id, inverse_of: :object_sequence
    has_many sequences, class_name: 'Sequence', through: relationships, source: :subject_sequence, inverse_of: :sequences

    accepts_nested_attributes_for sequences
    accepts_nested_attributes_for relationships
  end

  validates_presence_of :sequence
  validates_inclusion_of :sequence_type, in: ['DNA', 'RNA', 'AA']

  # @param used_on [String] required, one of `GeneAttribute` or `SequenceRelationship`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = nil)
    return Sequence.none if used_on.nil?
    t = case used_on
        when 'GeneAttribute'
          GeneAttribute.arel_table
        when 'SequenceRelationship'
          SequenceRelationship.arel_table
        end

    p = Sequence.arel_table

    # i is a select manager
    i = t.project(t['sequence_id'], t['updated_at']).from(t)
      .where(t['updated_at'].gt( 1.weeks.ago ))
      .where(t['updated_by_id'].eq(user_id))
      .where(t['project_id'].eq(project_id))
      .order(t['updated_at'].desc)

    # i is a select manager
    i = case used_on
        when 'SequenceRelationship'
          t.project(t['object_sequence_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'])
        else
          t.project(t['sequence_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'])
        end

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

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

    Sequence.joins(j).pluck(:sequence_id).uniq
  end

  # @params target [String] one of nil, 'SequenceRelationship', 'GeneAttribute'
  # @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 = {
      recent: [],
      quick: [],
      pinboard: Sequence.pinned_by(user_id).where(project_id: project_id).to_a
    }

    if r.empty?
      h[:quick] = Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a).uniq
    end

    h
  end

  protected

  def build_relationships
    describe_with.gene_attributes.each do |ga|
      related_sequence_relationships.build(subject_sequence: ga.sequence, type: ga.sequence_relationship_type)
    end
  end

  def normalize_sequence_type
    sequence_type.to_s.upcase! if sequence_type.present?
  end

end

#sequence ⇒ String

Returns the letters representing the sequence.

Returns:

  • (String) —

    the letters representing the sequence



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# File 'app/models/sequence.rb', line 22

class Sequence < ApplicationRecord

  include Housekeeping

  include Shared::AlternateValues
  include Shared::DataAttributes
  include Shared::Confidences
  include Shared::Documentation
  include Shared::Identifiers
  include Shared::Notes
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::HasPapertrail
  include Shared::IsData

  is_origin_for 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Sequence'

  ALTERNATE_VALUES_FOR = [:name].freeze

  # Pass a Gene::Descriptor instance to clone that description to this sequence
  attr_accessor :describe_with

  has_many :sequence_relationships, foreign_key: :subject_sequence_id, inverse_of: :subject_sequence # this sequence describes others
  has_many :sequences, through: :sequence_relationships, source: :object_sequence

  has_many :related_sequence_relationships, class_name: 'SequenceRelationship', foreign_key: :object_sequence_id, inverse_of: :object_sequence # attributes of this sequence
  has_many :related_sequences, through: :related_sequence_relationships, source: :subject_sequence
  has_many :gene_attributes, inverse_of: :sequence

  # has_many :descriptors, through: :gene_attributes, inverse_of: :sequences, as: 'Descriptor::Gene'

  before_validation :build_relationships, if: -> {describe_with.present?}
  before_validation :normalize_sequence_type

  SequenceRelationship.descendants.each do |d|
    t = d.name.demodulize.tableize.singularize
    relationships = "#{t}_relationships".to_sym
    sequences = "#{t}_sequences".to_sym

    has_many relationships, class_name: d.name.to_s, foreign_key: :object_sequence_id, inverse_of: :object_sequence
    has_many sequences, class_name: 'Sequence', through: relationships, source: :subject_sequence, inverse_of: :sequences

    accepts_nested_attributes_for sequences
    accepts_nested_attributes_for relationships
  end

  validates_presence_of :sequence
  validates_inclusion_of :sequence_type, in: ['DNA', 'RNA', 'AA']

  # @param used_on [String] required, one of `GeneAttribute` or `SequenceRelationship`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = nil)
    return Sequence.none if used_on.nil?
    t = case used_on
        when 'GeneAttribute'
          GeneAttribute.arel_table
        when 'SequenceRelationship'
          SequenceRelationship.arel_table
        end

    p = Sequence.arel_table

    # i is a select manager
    i = t.project(t['sequence_id'], t['updated_at']).from(t)
      .where(t['updated_at'].gt( 1.weeks.ago ))
      .where(t['updated_by_id'].eq(user_id))
      .where(t['project_id'].eq(project_id))
      .order(t['updated_at'].desc)

    # i is a select manager
    i = case used_on
        when 'SequenceRelationship'
          t.project(t['object_sequence_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'])
        else
          t.project(t['sequence_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'])
        end

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

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

    Sequence.joins(j).pluck(:sequence_id).uniq
  end

  # @params target [String] one of nil, 'SequenceRelationship', 'GeneAttribute'
  # @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 = {
      recent: [],
      quick: [],
      pinboard: Sequence.pinned_by(user_id).where(project_id: project_id).to_a
    }

    if r.empty?
      h[:quick] = Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a).uniq
    end

    h
  end

  protected

  def build_relationships
    describe_with.gene_attributes.each do |ga|
      related_sequence_relationships.build(subject_sequence: ga.sequence, type: ga.sequence_relationship_type)
    end
  end

  def normalize_sequence_type
    sequence_type.to_s.upcase! if sequence_type.present?
  end

end

#sequence_type ⇒ String

Returns one of “DNA”, “RNA”, “AA”.

Returns:

  • (String) —

    one of “DNA”, “RNA”, “AA”



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# File 'app/models/sequence.rb', line 22

class Sequence < ApplicationRecord

  include Housekeeping

  include Shared::AlternateValues
  include Shared::DataAttributes
  include Shared::Confidences
  include Shared::Documentation
  include Shared::Identifiers
  include Shared::Notes
  include Shared::OriginRelationship
  include Shared::ProtocolRelationships
  include Shared::Tags
  include Shared::HasPapertrail
  include Shared::IsData

  is_origin_for 'Sequence'
  originates_from 'Extract', 'Specimen', 'Lot', 'RangedLot', 'Sequence'

  ALTERNATE_VALUES_FOR = [:name].freeze

  # Pass a Gene::Descriptor instance to clone that description to this sequence
  attr_accessor :describe_with

  has_many :sequence_relationships, foreign_key: :subject_sequence_id, inverse_of: :subject_sequence # this sequence describes others
  has_many :sequences, through: :sequence_relationships, source: :object_sequence

  has_many :related_sequence_relationships, class_name: 'SequenceRelationship', foreign_key: :object_sequence_id, inverse_of: :object_sequence # attributes of this sequence
  has_many :related_sequences, through: :related_sequence_relationships, source: :subject_sequence
  has_many :gene_attributes, inverse_of: :sequence

  # has_many :descriptors, through: :gene_attributes, inverse_of: :sequences, as: 'Descriptor::Gene'

  before_validation :build_relationships, if: -> {describe_with.present?}
  before_validation :normalize_sequence_type

  SequenceRelationship.descendants.each do |d|
    t = d.name.demodulize.tableize.singularize
    relationships = "#{t}_relationships".to_sym
    sequences = "#{t}_sequences".to_sym

    has_many relationships, class_name: d.name.to_s, foreign_key: :object_sequence_id, inverse_of: :object_sequence
    has_many sequences, class_name: 'Sequence', through: relationships, source: :subject_sequence, inverse_of: :sequences

    accepts_nested_attributes_for sequences
    accepts_nested_attributes_for relationships
  end

  validates_presence_of :sequence
  validates_inclusion_of :sequence_type, in: ['DNA', 'RNA', 'AA']

  # @param used_on [String] required, one of `GeneAttribute` or `SequenceRelationship`
  # @return [Scope]
  #   the max 10 most recently used otus, as `used_on`
  def self.used_recently(user_id, project_id, used_on = nil)
    return Sequence.none if used_on.nil?
    t = case used_on
        when 'GeneAttribute'
          GeneAttribute.arel_table
        when 'SequenceRelationship'
          SequenceRelationship.arel_table
        end

    p = Sequence.arel_table

    # i is a select manager
    i = t.project(t['sequence_id'], t['updated_at']).from(t)
      .where(t['updated_at'].gt( 1.weeks.ago ))
      .where(t['updated_by_id'].eq(user_id))
      .where(t['project_id'].eq(project_id))
      .order(t['updated_at'].desc)

    # i is a select manager
    i = case used_on
        when 'SequenceRelationship'
          t.project(t['object_sequence_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'])
        else
          t.project(t['sequence_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'])
        end

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

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

    Sequence.joins(j).pluck(:sequence_id).uniq
  end

  # @params target [String] one of nil, 'SequenceRelationship', 'GeneAttribute'
  # @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 = {
      recent: [],
      quick: [],
      pinboard: Sequence.pinned_by(user_id).where(project_id: project_id).to_a
    }

    if r.empty?
      h[:quick] = Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
    else
      h[:recent] = Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a
      h[:quick] = (Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
          Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a).uniq
    end

    h
  end

  protected

  def build_relationships
    describe_with.gene_attributes.each do |ga|
      related_sequence_relationships.build(subject_sequence: ga.sequence, type: ga.sequence_relationship_type)
    end
  end

  def normalize_sequence_type
    sequence_type.to_s.upcase! if sequence_type.present?
  end

end

Class Method Details

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

Returns otus optimized for user selection.

Returns:

  • (Hash) —

    otus optimized for user selection



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# File 'app/models/sequence.rb', line 129

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

  if r.empty?
    h[:quick] = Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a
  else
    h[:recent] = Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a
    h[:quick] = (Sequence.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
        Sequence.where('"sequences"."id" IN (?)', r.first(10) ).to_a).uniq
  end

  h
end

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

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

Parameters:

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

    required, one of ‘GeneAttribute` or `SequenceRelationship`

Returns:

  • (Scope) —

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



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# File 'app/models/sequence.rb', line 76

def self.used_recently(user_id, project_id, used_on = nil)
  return Sequence.none if used_on.nil?
  t = case used_on
      when 'GeneAttribute'
        GeneAttribute.arel_table
      when 'SequenceRelationship'
        SequenceRelationship.arel_table
      end

  p = Sequence.arel_table

  # i is a select manager
  i = t.project(t['sequence_id'], t['updated_at']).from(t)
    .where(t['updated_at'].gt( 1.weeks.ago ))
    .where(t['updated_by_id'].eq(user_id))
    .where(t['project_id'].eq(project_id))
    .order(t['updated_at'].desc)

  # i is a select manager
  i = case used_on
      when 'SequenceRelationship'
        t.project(t['object_sequence_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'])
      else
        t.project(t['sequence_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'])
      end

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

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

  Sequence.joins(j).pluck(:sequence_id).uniq
end

Instance Method Details

#build_relationships ⇒ Object (protected) 



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# File 'app/models/sequence.rb', line 150

def build_relationships
  describe_with.gene_attributes.each do |ga|
    related_sequence_relationships.build(subject_sequence: ga.sequence, type: ga.sequence_relationship_type)
  end
end

#normalize_sequence_type ⇒ Object (protected) 



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# File 'app/models/sequence.rb', line 156

def normalize_sequence_type
  sequence_type.to_s.upcase! if sequence_type.present?
end