Class: SqedDepiction

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

Overview

A SqedDepiction identifies a depiction as sqed (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::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) 


36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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) 


36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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) 


36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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) 


36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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.



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

def rebuild
  @rebuild
end

#result_boundaries ⇒ Hash

Returns A cache for the result.

Returns:

  • (Hash) —

    A cache for the result



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
 
# File 'app/models/sqed_depiction.rb', line 36

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

  attr_accessor :rebuild

  belongs_to :depiction
  has_one :image, through: :depiction

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

  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

  after_save :recalculate, if: -> { rebuild }

  def rebuild=(value)
    @rebuild = value
  end

  def recalculate
    preprocess(true)
  end

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

  def depiction_object
    depiction.depiction_object
  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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
    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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
    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: 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: 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: 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: project_id).where('id > ?', id).order(:id).limit(1)
    sd.any? ? sd.first : SqedDepiction.where(project_id: project_id).first
  end

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

    # otherwise rebuild
    result = 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

.clear_stale_progress(sqed_depiction = nil) ⇒ Object 



116
117
118
119
120
121
122
123
124
125
 
# File 'app/models/sqed_depiction.rb', line 116

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

.last_without_data(project_id) ⇒ Object 



127
128
129
130
 
# File 'app/models/sqed_depiction.rb', line 127

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: 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



182
183
184
185
186
187
188
189
190
191
192
 
# File 'app/models/sqed_depiction.rb', line 182

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 



81
82
83
84
85
86
87
88
 
# File 'app/models/sqed_depiction.rb', line 81

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 



90
91
92
93
94
95
96
97
 
# File 'app/models/sqed_depiction.rb', line 90

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



142
143
144
145
 
# File 'app/models/sqed_depiction.rb', line 142

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

#depiction_is_of_collection_object ⇒ Object (protected) 



196
197
198
199
200
 
# File 'app/models/sqed_depiction.rb', line 196

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

#depiction_object ⇒ Object 



77
78
79
 
# File 'app/models/sqed_depiction.rb', line 77

def depiction_object
  depiction.depiction_object
end

#extraction_metadata ⇒ Object 



67
68
69
70
71
72
73
74
75
 
# File 'app/models/sqed_depiction.rb', line 67

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

#is_in_progress? ⇒ Boolean

Returns:

  • (Boolean) 


112
113
114
 
# File 'app/models/sqed_depiction.rb', line 112

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

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



147
148
149
150
151
152
153
154
155
156
157
158
159
 
# File 'app/models/sqed_depiction.rb', line 147

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



134
135
136
137
138
 
# File 'app/models/sqed_depiction.rb', line 134

def next_collection_object
  object = CollectionObject.joins(:sqed_depictions).where(project_id: 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 



161
162
163
164
 
# File 'app/models/sqed_depiction.rb', line 161

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



101
102
103
104
105
106
107
108
109
110
 
# File 'app/models/sqed_depiction.rb', line 101

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.nil? ? SqedDepiction.where(in_progress: false, project_id: project_id).order(:id).first : object
  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.nil? ? SqedDepiction.where(project_id: project_id).order(:id).first : object
  end
end

#preprocess(force = true) ⇒ Object 



166
167
168
169
170
171
172
173
174
175
176
177
178
 
# File 'app/models/sqed_depiction.rb', line 166

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

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

#recalculate ⇒ Object 



63
64
65
 
# File 'app/models/sqed_depiction.rb', line 63

def recalculate
  preprocess(true)
end

#sqed_metadata_map ⇒ Object (protected) 



202
203
204
 
# File 'app/models/sqed_depiction.rb', line 202

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