Class: SqedDepiction

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::IsData, Shared::Notes, Shared::Tags
Defined in:
app/models/sqed_depiction.rb

Overview

A SqedDepiction identifies a depiction as sqed (https://github.com/SpeciesFileGroup/sqed) parsable, and records the metadata required for parsing a stage image.

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_in_use?, #similar

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Tags

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

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#boundary_color ⇒ Symbol

Color of the boundaries in the image, default/recommendation is green.

Returns:

  • (Symbol) 


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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#boundary_finder ⇒ String

Name of the sqed BoundaryFinder class to use, e.g. 'Sqed::BoundaryFinder::ColorLineFinder'

Returns:

  • (String) 


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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#has_border ⇒ Boolean

Returns True if the stage image has a border than needs to be detected.

Returns:

  • (Boolean) —

    True if the stage image has a border than needs to be detected



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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#layout ⇒ Symbol

The Sqed layout, like :cross, :equal_cross, :vertical_offset_cross, :internal_box etc.

Returns:

  • (Symbol) 


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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#metadata_map ⇒ Hash

The sqed metadata map, e.g. {0 => :curator_metadata, 1 => :identifier, 2 => :image_registration, 3 => :annotated_specimen }.

Returns:

  • (Hash) 


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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#rebuild ⇒ Object

Returns the value of attribute rebuild.



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

def rebuild
  @rebuild
end

#result_boundaries ⇒ Hash

Returns A cache for the result.

Returns:

  • (Hash) —

    A cache for the result



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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#result_ocr ⇒ Hash

Returns A cache for the ocr result.

Returns:

  • (Hash) —

    A cache for the ocr result



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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

#specimen_coordinates ⇒ Hash

Returns Not presently used, the specific coordinates bounding the specimen(s) only.

Returns:

  • (Hash) —

    Not presently used, the specific coordinates bounding the specimen(s) only



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# File 'app/models/sqed_depiction.rb', line 36

class SqedDepiction < ApplicationRecord
  include Housekeeping
  include Shared::Tags
  include Shared::Notes

  # True?!
  include Shared::IsData

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

  has_one :collection_object, through: :depiction, source_type: 'CollectionObject', source: :depiction_object, inverse_of: :sqed_depictions

  validates_presence_of :depiction
  validates_presence_of  :metadata_map, :boundary_color
  validates_inclusion_of :layout, in: SqedConfig::LAYOUTS.keys.map(&:to_s)
  validates_inclusion_of :boundary_finder, in: %w{Sqed::BoundaryFinder::ColorLineFinder Sqed::BoundaryFinder::Cross}
  validates_inclusion_of :has_border, in: [true, false]
  validate :depiction_is_of_collection_object

  accepts_nested_attributes_for :depiction

  before_validation :set_invisible_boundary, if: -> { layout.presence == 'stage' }

  def set_invisible_boundary
    self.boundary_color = 'invisible'
  end

  after_save :recalculate, if: -> { rebuild }
  after_create_commit :enqueue_preprocess

  def self.is_containable?
    false
  end

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

  def enqueue_preprocess
    SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
  end

  def extraction_metadata
    {
      boundary_color: boundary_color.to_sym,
      boundary_finder: boundary_finder&.constantize,
      has_border:,
      layout: layout.to_sym,
      metadata_map: sqed_metadata_map
    }
  end

  delegate :depiction_object, to: :depiction

  def self.annotates?
    false
  end

  def self.with_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].not_eq(nil).
      or(t[:buffered_determinations].not_eq(nil)).
      or(t[:buffered_other_labels].not_eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  def self.without_collection_object_data
    t = CollectionObject.arel_table
    q = t[:buffered_collecting_event].eq(nil).
      and(t[:buffered_determinations].eq(nil)).
      and(t[:buffered_other_labels].eq(nil))

    joins(:collection_object).where(q.to_sql)
  end

  # @return [SqedDepiction]
  #   the next record in which the collection object has no buffered data
  def next_without_data(progress = false)
    if progress
      SqedDepiction.clear_stale_progress(self)
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
    else
      object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
      object || SqedDepiction.where(project_id:).order(:id).first
    end
  end

  def is_in_progress?
    in_progress && in_progress < 5.minutes.ago
  end

  def self.clear_stale_progress(sqed_depiction = nil)
    SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
      .update_all(in_progress: nil)
    if sqed_depiction
      SqedDepiction
        .where(updated_by_id: sqed_depiction.updated_by_id)
        .update_all(in_progress: nil)
    end
    true
  end

  def self.last_without_data(project_id)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
    object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
  end

  # @return [CollectionObject, nil]
  #    the next collection object, by :id, created from the addition of a SqedDepiction
  def next_collection_object
    object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
    object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
    object
  end

  # @return [Array of symbols]
  #   the (named) sections in this depiction that may have collecting event label metadata
  def collecting_event_sections
    # !! master merge
    [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
  end

  def nearby_sqed_depictions(before = 5, after = 5, progress = false)
    q = SqedDepiction.where(project_id:)

    if progress == true
      SqedDepiction.clear_stale_progress(self)
      q = q.where(in_progress: nil)
    end

    a = q.where('id > ?', id).order(:id).limit(after)
    b = q.where('id < ?', id).order('id DESC').limit(before)

    return { before: b, after: a}
  end

  def next_sqed_depiction
    sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id:).first
  end

  def preprocess(force = true)
    return true if !File.exist?(depiction.image.image_file.path(:original))
    # don't rebuild if not forced and one or both cache is empty
    if !force
      if result_ocr.present? || result_boundary_coordinates.present?
        return true
      end
    end

    # otherwise rebuild
    result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
    result.cache_all
  end

  # @return [Integer]
  #   caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes
  def self.preprocess_empty(total = 10)
    t = SqedDepiction.arel_table
    i = 0
    while i < total
      r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
      return i if r.nil?
      r.preprocess
      i = i + 1
    end
    i
  end

  protected

  def depiction_is_of_collection_object
    if depiction
      errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
    end
  end

  def sqed_metadata_map
    metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
  end

end

Class Method Details

.annotates? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/sqed_depiction.rb', line 97

def self.annotates?
  false
end

.clear_stale_progress(sqed_depiction = nil) ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 136

def self.clear_stale_progress(sqed_depiction = nil)
  SqedDepiction.where('(in_progress < ?)', 5.minutes.ago)
    .update_all(in_progress: nil)
  if sqed_depiction
    SqedDepiction
      .where(updated_by_id: sqed_depiction.updated_by_id)
      .update_all(in_progress: nil)
  end
  true
end

.is_containable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/sqed_depiction.rb', line 69

def self.is_containable?
  false
end

.last_without_data(project_id) ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 147

def self.last_without_data(project_id)
  object = SqedDepiction.without_collection_object_data.with_project_id(project_id).order(:id).first
  object.nil? ? SqedDepiction.where(project_id:).order(id: :asc).first : object
end

.preprocess_empty(total = 10) ⇒ Integer

Returns caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes.

Returns:

  • (Integer) —

    caches section coordinates and ocr text for the first images that don't have such caches !! does not take into account project or user, just finds and processes



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# File 'app/models/sqed_depiction.rb', line 202

def self.preprocess_empty(total = 10)
  t = SqedDepiction.arel_table
  i = 0
  while i < total
    r = SqedDepiction.where(t[:result_ocr].eq(nil).or(t[:result_boundary_coordinates].eq(nil)).to_sql).limit(1).first
    return i if r.nil?
    r.preprocess
    i = i + 1
  end
  i
end

.with_collection_object_data ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 101

def self.with_collection_object_data
  t = CollectionObject.arel_table
  q = t[:buffered_collecting_event].not_eq(nil).
    or(t[:buffered_determinations].not_eq(nil)).
    or(t[:buffered_other_labels].not_eq(nil))

  joins(:collection_object).where(q.to_sql)
end

.without_collection_object_data ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 110

def self.without_collection_object_data
  t = CollectionObject.arel_table
  q = t[:buffered_collecting_event].eq(nil).
    and(t[:buffered_determinations].eq(nil)).
    and(t[:buffered_other_labels].eq(nil))

  joins(:collection_object).where(q.to_sql)
end

Instance Method Details

#collecting_event_sections ⇒ Array of symbols

Returns the (named) sections in this depiction that may have collecting event label metadata.

Returns:

  • (Array of symbols) —

    the (named) sections in this depiction that may have collecting event label metadata



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# File 'app/models/sqed_depiction.rb', line 162

def collecting_event_sections
  # !! master merge
  [:collecting_event_labels, :annotated_specimen] & extraction_metadata[:metadata_map].values
end

#depiction_is_of_collection_object ⇒ Object (protected) 



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# File 'app/models/sqed_depiction.rb', line 216

def depiction_is_of_collection_object
  if depiction
    errors.add(:depiction, 'must be of a collection object') if !(depiction.depiction_object_type =~ /CollectionObject/)
  end
end

#enqueue_preprocess ⇒ Object 



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

def enqueue_preprocess
  SqedDepictionPreprocessJob.perform_later(sqed_depiction_id: id)
end

#extraction_metadata ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 85

def extraction_metadata
  {
    boundary_color: boundary_color.to_sym,
    boundary_finder: boundary_finder&.constantize,
    has_border:,
    layout: layout.to_sym,
    metadata_map: sqed_metadata_map
  }
end

#is_in_progress? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/sqed_depiction.rb', line 132

def is_in_progress?
  in_progress && in_progress < 5.minutes.ago
end

#nearby_sqed_depictions(before = 5, after = 5, progress = false) ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 167

def nearby_sqed_depictions(before = 5, after = 5, progress = false)
  q = SqedDepiction.where(project_id:)

  if progress == true
    SqedDepiction.clear_stale_progress(self)
    q = q.where(in_progress: nil)
  end

  a = q.where('id > ?', id).order(:id).limit(after)
  b = q.where('id < ?', id).order('id DESC').limit(before)

  return { before: b, after: a}
end

#next_collection_object ⇒ CollectionObject?

Returns the next collection object, by :id, created from the addition of a SqedDepiction.

Returns:

  • (CollectionObject, nil) —

    the next collection object, by :id, created from the addition of a SqedDepiction



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# File 'app/models/sqed_depiction.rb', line 154

def next_collection_object
  object = CollectionObject.joins(:sqed_depictions).where(project_id:).where('sqed_depictions.id > ?', id).where('collection_objects.id <> ?', depiction_object.id).order(:id).first
  object = CollectionObject.joins(:sqed_depictions).order(:id).first if object.nil?
  object
end

#next_sqed_depiction ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 181

def next_sqed_depiction
  sd = SqedDepiction.where(project_id:).where('id > ?', id).order(:id).limit(1)
  sd.any? ? sd.first : SqedDepiction.where(project_id:).first
end

#next_without_data(progress = false) ⇒ SqedDepiction

Returns the next record in which the collection object has no buffered data.

Returns:

  • (SqedDepiction) —

    the next record in which the collection object has no buffered data



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# File 'app/models/sqed_depiction.rb', line 121

def next_without_data(progress = false)
  if progress
    SqedDepiction.clear_stale_progress(self)
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
    object || SqedDepiction.where(in_progress: nil, project_id:).order(:id).first
  else
    object = SqedDepiction.without_collection_object_data.with_project_id(project_id).where('collection_objects.id <> ?', depiction_object.id).where('sqed_depictions.id > ?', id).order(:id).first
    object || SqedDepiction.where(project_id:).order(:id).first
  end
end

#preprocess(force = true) ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 186

def preprocess(force = true)
  return true if !File.exist?(depiction.image.image_file.path(:original))
  # don't rebuild if not forced and one or both cache is empty
  if !force
    if result_ocr.present? || result_boundary_coordinates.present?
      return true
    end
  end

  # otherwise rebuild
  result = Vendor::SqedToTaxonworks::Result.new(depiction_id: depiction.id)
  result.cache_all
end

#recalculate ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 77

def recalculate
  preprocess(true)
end

#set_invisible_boundary ⇒ Object 



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# File 'app/models/sqed_depiction.rb', line 62

def set_invisible_boundary
  self.boundary_color = 'invisible'
end

#sqed_metadata_map ⇒ Object (protected) 



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# File 'app/models/sqed_depiction.rb', line 222

def sqed_metadata_map
  metadata_map.inject({}){|hsh, i| hsh.merge(i[0].to_i => i[1].to_sym)}
end