Class: CaTissue::SpecimenCollectionGroup

Inherits:
Object
  • Object
show all
Includes:
CaRuby::Resource::Unique, Resource
Defined in:
lib/catissue/domain/specimen_collection_group.rb,
lib/catissue/domain/uniquify.rb,
lib/catissue/migration/shims.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.

Constant Summary collapse 

[:consent_tier_statuses]
@@diagnosis_cv_finder = 
nil

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Resource

#database, included, #tolerant_match?

Methods included from Annotatable

#annotation_proxy, #create_proxy, #method_missing

Constructor Details

#initialize(params = nil) ⇒ SpecimenCollectionGroup

caTissue alert - Bug #64: Initialize the SCG consent_tier_statuses to an empty set.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 110

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

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class CaTissue::Annotatable

Class Method Details

.diagnosis_controlled_value(value) ⇒ Object

Returns the diagnosis controlled value as follows:

  • If CV lookup is disabled, then this method returns value.

  • Otherwise, if the value is remapped via a configuration remap file, then this method returns the remapped CV.

  • Otherwise, if the value is a valid CV, then this method returns value.

  • Otherwise, this method returns nil.



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# File 'lib/catissue/migration/shims.rb', line 21

def self.diagnosis_controlled_value(value)
  @@diagnosis_cv_finder.nil? ? value : @@diagnosis_cv_finder.controlled_value(value)
end

.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

Instance Method Details

#autogenerated?(operation) ⇒ Boolean

Relaxes the CaRuby::Persistable#saved_fetch_attributes 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 275

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

#collect(params) ⇒ Object

Collects and receives this SCG with the given params option => value hash. The SCG collection status is set to ‘Completed’.

Supported parameters are as follows:

  • receiver - the required User who received the specimens

  • received_date - the optional receival date (default is now)

  • collector - the optional User who collected the specimens (default is receiver)

  • collection_date - the optional collection date (default is received_date)

If there is at least a receiver, then no additional event parameters are added.

Raises ValidationError if this SCG has already been received.

Raises:

  • (ValidationError) 


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# File 'lib/catissue/domain/specimen_collection_group.rb', line 180

def collect(params)
  raise ValidationError.new("SCG is already collected") if received?
  specimen_event_parameters.merge!(extract_event_params(params))
end

#collected? ⇒ Boolean

Returns whether this SCG has a collected event.

Returns:

  • (Boolean) 


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# File 'lib/catissue/domain/specimen_collection_group.rb', line 190

def collected?
  collection_event_parameters
end

#collection_event_parameters ⇒ Object

Returns the CollectionEventParameters for this specimen group.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 207

def collection_event_parameters
  event_parameters.detect { |ep| CaTissue::CollectionEventParameters === ep }
end

#collection_protocol ⇒ CollectionProtocol

Returns the SCG CPE CP.

Returns:



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 117

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

#collection_timestamp ⇒ Date

Returns the date this SCG was donated by the participant.

Returns:

  • (Date) —

    the date this SCG was donated by the participant.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 201

def collection_timestamp
  ep = collection_event_parameters
  ep.timestamp if ep
end

#collector ⇒ Object

Returns the User who collected this SCG.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 195

def collector
  ep = collection_event_parameters
  ep.user if ep
end

#consent_tier_statuses ⇒ Java::JavaUtil::Set

caTissue alert - Bug #64: Some domain collection properties not initialized. Initialize consent_tier_statuses if necessary.

Returns:

  • (Java::JavaUtil::Set) —

    the statuses



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 18

def consent_tier_statuses
  getConsentTierStatusCollection or (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 142

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

#direct_dependents(attribute) ⇒ Object

Overrides CaRuby::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 236

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 122

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 246

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

#merge_attributes(other, attributes = nil) ⇒ Object

Merges the other object into this SpecimenCollectionGroup. This method overrides the standard CaRuby::Resource#merge_attributes method as follows:

  • Builds the SpecimenEventParameter objects from atomic parameters, e.g.:

    SpecimenCollectionGroup.create(:name = > name, ..., :collector => collector, :receiver => receiver)

    The supported event parameters are described in #collect.

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



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 152

def merge_attributes(other, attributes=nil)
  if Hash === other then
    # extract the event parameters
    other[:specimen_event_parameters] = extract_event_params(other)
    # 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 super for standard attribute value merge
  super
end

#migrate_clinical_diagnosis(value, row) ⇒ Object

Returns the #diagnosis_controlled_value.



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# File 'lib/catissue/migration/shims.rb', line 26

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 230

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 132

def pending?
  collection_status =~ /^Pending/
end

#protocol ⇒ Object 



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 185

def protocol
  collection_event.protocol if collection_event
end

#received? ⇒ Boolean

Returns whether this SCG has a received event.

Returns:

  • (Boolean) 


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# File 'lib/catissue/domain/specimen_collection_group.rb', line 212

def received?
  received_event_parameters
end

#received_event_parameters ⇒ Object

Returns the ReceivedEventParameters for this specimen group.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 223

def received_event_parameters
  event_parameters.detect { |ep| CaTissue::ReceivedEventParameters === ep }
end

#receiver ⇒ Object

Returns the User who received this specimen group.



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 217

def receiver
  ep = received_event_parameters
  ep.user if ep
end

#requirements ⇒ <SpecimenRequirement>

Returns the SCG CPE requirements.

Returns:



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 127

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

#saved_fetch_attributes(operation) ⇒ Object

Relaxes the CaRuby::Persistable#saved_fetch_attributes 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 266

def saved_fetch_attributes(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 137

def size
  specimens.size
end

#surgical_pathology_number=(value) ⇒ Object

Converts an Integer SPN value to a String.

Parameters:

  • value (Numeric, String) —

    the SPN value



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 37

def surgical_pathology_number=(value)
  value = value.to_s if Numeric === value
  setSurgicalPathologyNumber(value)
end

#uniquify ⇒ Object

Makes this SCG’s SPN unique.



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# File 'lib/catissue/domain/uniquify.rb', line 44

def uniquify
  super
  oldval = surgical_pathology_number || return
  newval = uniquify_value(oldval)
  self.surgical_pathology_number = newval
  logger.debug { "Reset #{qp} SPN from #{oldval} to unique value #{newval}." }
end

#validate ⇒ Object 



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# File 'lib/catissue/domain/specimen_collection_group.rb', line 255

def validate
  super
  validate_consent
  validate_event_parameters
end