Class: CaTissue::SpecimenCollectionGroup

Inherits:
Object
  • Object
show all
Includes:
Collectible, Jinx::Unique
Defined in:
lib/catissue/domain/specimen_collection_group.rb,
lib/catissue/migration/shims.rb,
lib/catissue/migration/unique.rb,
lib/catissue/migration/migratable.rb,
lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb,
lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb

Overview

The SpecimenCollectionGroup domain class.

Note: the SpecimenCollectionGroup name attribute is auto-generated on create in caTissue 1.1 API and should not be set by API clients when creating a new SpecimenCollectionGroup in the database.

Defined Under Namespace

Modules: Pathology

Constant Summary collapse 

[:consent_tier_statuses]
@@diagnosis_cv_finder = 
nil

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Collectible

#collect, #collected?, #collectible_event_parameters, #collection_event_parameters, #collection_timestamp, #collector, #received?, #received_event_parameters, #receiver

Constructor Details

#initialize ⇒ SpecimenCollectionGroup

Returns a new instance of SpecimenCollectionGroup.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 104

def initialize
  super
  # work around caTissue Bug #64
  self.consent_tier_statuses ||= Java::JavaUtil::LinkedHashSet.new
end

Class Method Details

.diagnosis_cv_finder=(finder) ⇒ Object

Sets this SpecimenCollectionGroup diagnosis ControlledValueFinder.



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# File 'lib/catissue/migration/shims.rb', line 11

def self.diagnosis_cv_finder=(finder)
  @@diagnosis_cv_finder = finder
end

.enable_cv_finder ⇒ Object

Enables diagnosis controlled value lookup.



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# File 'lib/catissue/migration/migratable.rb', line 28

def self.enable_cv_finder
  @diagnosis_cv_finder ||= ControlledValueFinder.new(:clinical_diagnosis)
end

Instance Method Details

#autogenerated?(operation) ⇒ Boolean

Relaxes the CaRuby::Persistable.saved_attributes_to_fetch condition for a SCG as follows:

  • If the SCG status was updated from Pending to Collected, then fetch the saved SCG event parameters.

Returns:

  • (Boolean) 


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# File 'lib/catissue/domain/specimen_collection_group.rb', line 206

def autogenerated?(operation)
  operation == :update && status_changed_to_complete? ? EVENT_PARAM_ATTRS : super
end

#collection_protocol ⇒ CollectionProtocol

Returns the SCG CPE CP.

Returns:



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 111

def collection_protocol
  collection_protocol_event.collection_protocol if collection_protocol_event
end

#collection_status=(value) ⇒ Object

Sets the collection status for this SCG. If the SCG status is set to Complete, then the status of each of the SCG Specimens with status Pending is reset to Collected.

Parameters:

  • value (String) —

    a permissible SCG status



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 27

def collection_status=(value)
  if value == 'Complete' then
    specimens.each { |spc| spc.collection_status = 'Collected' if spc.pending? }
  end
  setCollectionStatus(value)
end

#consent_tier_statuses ⇒ Java::JavaUtil::Set

Returns the statuses.

Returns:

  • (Java::JavaUtil::Set) —

    the statuses



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 17

def consent_tier_statuses
  ctss = getConsentTierStatusCollection
  ctss ||= self.consent_tier_statuses = Java::JavaUtil::LinkedHashSet.new
end

#delete ⇒ Object

Removes associations to this registration.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 136

def delete
  registration.specimen_collection_groups.delete(self) if registration
end

#direct_dependents(attribute) ⇒ Object

Overrides Jinx::Resource.direct_dependents in the case of the specimens attribute to select only top-level Specimens not derived from another Specimen.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 173

def direct_dependents(attribute)
  if attribute == :specimens then
    super.reject { |spc| spc.parent }
  else
    super
  end
end

#event_point ⇒ Double?

Returns the SCG CPE event point.

Returns:

  • (Double, nil) —

    the SCG CPE event point



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 116

def event_point
  collection_protocol_event and collection_protocol_event.study_calendar_event_point
end

#mandatory_attributes ⇒ Object 



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 183

def mandatory_attributes
  pas = super
  if registration and not registration.consent_tier_responses.empty? then
    pas + CONSENT_TIER_STATUS_ATTRS
  else
    pas
  end
end

#merge_attributes(other, attributes = nil, matches = nil, &filter) ⇒ Object

Merges the other object into this SpecimenCollectionGroup. This method augments Collectible#merge_attributes as follows:

  • Adds the transitive closure of each non-derived Specimen in the source.

Parameters:

  • other (Collectible, {Symbol => Object}) —

    other the source object or Hash

  • opts (Hash) —

    a customizable set of options

Options Hash (other):

  • :specimen_event_parameters (Enumerable) —

    the optional SEP merge collection to augment

  • :receiver (CaTissue::User) —

    the tissue bank user who received the tissue

  • :received_date (Date) —

    the received date (defaults to now)

  • :collector (CaTissue::User) —

    the user who acquired the tissue (defaults to the receiver)



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 146

def merge_attributes(other, attributes=nil, matches=nil, &filter)
  if Hash === other then
    # take the transitive closure of the specimens
    spcs = other.delete(:specimens)
    if spcs then
      spcs = [spcs] if CaTissue::Specimen === spcs
      # take the transitive closure of the root specimens in the hierarchy
      other[:specimens] = spcs.select { |spc| spc.parent.nil? }.transitive_closure(:children)
    end
  end
  # delegate to Collectible
  super
end

#migrate_clinical_diagnosis(value, row) ⇒ String

Returns the diagnosis controlled value.

Returns:

  • (String) —

    the diagnosis controlled value

Raises:

  • (Jinx::MigrationError) —

    if the value is not supported



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# File 'lib/catissue/migration/shims.rb', line 29

def migrate_clinical_diagnosis(value, row)
  SpecimenCollectionGroup.diagnosis_controlled_value(value)
end

#minimal_match?(other) ⇒ Boolean

Returns whether this SCG is the same as the other SCG in the scope of an existing parent CPR. This method returns whether the other SCG status is Pending and the event point is the same as the other event point.

Returns:

  • (Boolean) 


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# File 'lib/catissue/domain/specimen_collection_group.rb', line 167

def minimal_match?(other)
  super and event_point == other.event_point
end

#pending? ⇒ Boolean

Returns whether this SCG collection status is one of the Pending statuses.

Returns:

  • (Boolean) —

    whether this SCG collection status is one of the Pending statuses.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 126

def pending?
  collection_status =~ /^Pending/
end

#protocol ⇒ Object 



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 160

def protocol
  collection_event.protocol if collection_event
end

#requirements ⇒ <SpecimenRequirement>

Returns the SCG CPE requirements.

Returns:



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 121

def requirements
  collection_protocol_event.nil? ? Array::EMPTY_ARRAY : collection_protocol_event.requirements
end

#saved_attributes_to_fetch(operation) ⇒ Object

Relaxes the CaRuby::Persistable.saved_attributes_to_fetch condition for a SCG as follows:

  • If the SCG status was updated from Pending to Collected, then fetch the saved SCG event parameters.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 197

def saved_attributes_to_fetch(operation)
  operation == :update && status_changed_to_complete? ? EVENT_PARAM_ATTRS : super
end

#size ⇒ Object

Returns the number of specimens in this SpecimenCollectionGroup.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 131

def size
  specimens.size
end