Class: Extract

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

Overview

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

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

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

Methods included from SoftValidation

#clear_soft_validations, #fix_for, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations, #soft_validators

Methods included from Shared::HasRoles

#has_roles?

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Containable

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

Methods included from Shared::OriginRelationship

#new_objects, #old_objects, #reject_origin_relationships, #set_origin

Methods included from Shared::ProtocolRelationships

#protocolled?, #reject_protocols

Methods included from Shared::Identifiers

#identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#day_made ⇒ Integer

Returns 2 digit day the extract originated.

Returns:

  • (Integer) —

    2 digit day the extract originated



20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
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
 
# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::DataAttributes
  include Shared::HasRoles
  include SoftValidation
  include Shared::IsData

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

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true
  
  # Upstream 
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'


  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

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


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

  protected

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

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

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
              )
            )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

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

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['biological_collection_object_id'].eq(p['id']))) # !! note it's not biological_collection_object_id
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Extract.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

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

    h
  end

end

#is_made_now ⇒ Object

Returns the value of attribute is_made_now.



48
49
50
 
# File 'app/models/extract.rb', line 48

def is_made_now
  @is_made_now
end

#month_made ⇒ Integer

Returns 2 digit month the extract originated.

Returns:

  • (Integer) —

    2 digit month the extract originated



20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
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
 
# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::DataAttributes
  include Shared::HasRoles
  include SoftValidation
  include Shared::IsData

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

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true
  
  # Upstream 
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'


  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

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


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

  protected

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

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

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
              )
            )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

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

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['biological_collection_object_id'].eq(p['id']))) # !! note it's not biological_collection_object_id
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Extract.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

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

    h
  end

end

#verbatim_anatomical_origin ⇒ String

Returns proxy for a OriginRelationship to an AnatomicalClass.

Returns:

  • (String) —

    proxy for a OriginRelationship to an AnatomicalClass



20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
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
 
# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::DataAttributes
  include Shared::HasRoles
  include SoftValidation
  include Shared::IsData

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

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true
  
  # Upstream 
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'


  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

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


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

  protected

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

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

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
              )
            )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

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

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['biological_collection_object_id'].eq(p['id']))) # !! note it's not biological_collection_object_id
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Extract.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

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

    h
  end

end

#year_made ⇒ Integer

Returns 4 digit year the extract originated.

Returns:

  • (Integer) —

    4 digit year the extract originated



20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
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
 
# File 'app/models/extract.rb', line 20

class Extract < ApplicationRecord
  include Housekeeping
  include Shared::Identifiers
  include Shared::ProtocolRelationships
  include Shared::OriginRelationship
  include Shared::Containable
  include Shared::DataAttributes
  include Shared::HasRoles
  include SoftValidation
  include Shared::IsData

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

  belongs_to :repository, inverse_of: :extracts

  has_many :extractor_roles, -> { order('roles.position ASC') }, class_name: 'Extractor', as: :role_object, dependent: :destroy, validate: true
  has_many :extractors, -> { order('roles.position ASC') }, through: :extractor_roles, source: :person, validate: true
  
  # Upstream 
  has_many :otus, through: :related_origin_relationships, source: :old_object, source_type: 'Otu'
  has_many :collection_objects, through: :related_origin_relationships, source: :old_object, source_type: 'CollectionObject'

  # Downstresm
  has_many :sequences, through: :origin_relationships, source: :new_object, source_type: 'Sequence'
  has_many :extracts, through: :related_origin_relationships, source: :old_object, source_type: 'Extract'


  attr_accessor :is_made_now

  before_validation :set_made, if: -> {is_made_now}

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


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

  protected

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

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

    p = CollectionObject.arel_table

    # i is a select manager
    i = case used_on
        when 'BiologicalAssociation'
          t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
            .where(
              t['updated_at'].gt(1.weeks.ago).and(
                t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
              )
            )
              .where(t['created_by_id'].eq(user_id))
              .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        else
          t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
            .where(t['updated_at'].gt( 1.weeks.ago ))
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
            .order(t['updated_at'].desc)
        end

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

    j = case used_on
        when 'BiologicalAssociation'
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
            z['biological_association_subject_id'].eq(p['id'])
          ))
        else
          Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['biological_collection_object_id'].eq(p['id']))) # !! note it's not biological_collection_object_id
        end

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

  # @params target [String] one of `TaxonDetermination`, `BiologicalAssociation` , nil
  # @return [Hash] otus optimized for user selection
  def self.select_optimized(user_id, project_id, target = nil)
    r = used_recently(user_id, project_id, target)
    h = {
      quick: [],
      pinboard: Extract.pinned_by(user_id).where(project_id: project_id).to_a,
      recent: []
    }

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

    h
  end

end

Class Method Details

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

Returns otus optimized for user selection.

Returns:

  • (Hash) —

    otus optimized for user selection



125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
 
# File 'app/models/extract.rb', line 125

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

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

  h
end

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

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

Parameters:

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

    required, one of `Protocol`, `OriginRelationship`

Returns:

  • (Scope) —

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



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

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

  p = CollectionObject.arel_table

  # i is a select manager
  i = case used_on
      when 'BiologicalAssociation'
        t.project(t['biological_association_subject_id'], t['updated_at']).from(t)
          .where(
            t['updated_at'].gt(1.weeks.ago).and(
              t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
            )
          )
            .where(t['created_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      else
        t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
          .where(t['updated_at'].gt( 1.weeks.ago ))
          .where(t['created_by_id'].eq(user_id))
          .where(t['project_id'].eq(project_id))
          .order(t['updated_at'].desc)
      end

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

  j = case used_on
      when 'BiologicalAssociation'
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
          z['biological_association_subject_id'].eq(p['id'])
        ))
      else
        Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(z['biological_collection_object_id'].eq(p['id']))) # !! note it's not biological_collection_object_id
      end

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

Instance Method Details

#referenced_otus ⇒ Object

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

Returns:

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



59
60
61
62
63
64
 
# File 'app/models/extract.rb', line 59

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

#set_made ⇒ Object (protected) 



68
69
70
71
72
 
# File 'app/models/extract.rb', line 68

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