Class: CaTissue::CollectionProtocol

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

Overview

The CollectionProtocol domain class.

Instance Method Summary collapse

Methods included from Resource

#database, included, #tolerant_match?

Methods included from Annotatable

#annotation_proxy, #create_proxy, #method_missing

Methods included from HashCode

#==, #hash

Constructor Details

#initialize(params = nil) ⇒ CollectionProtocol

Returns a new instance of CollectionProtocol.



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

def initialize(params=nil)
  super
  respond_to?(:consent_tiers)
  # work around caTissue Bug #64 - consent tiers is nil rather than an empty set
  self.consent_tiers ||= Java::JavaUtil::LinkedHashSet.new
end

Dynamic Method Handling

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

Instance Method Details

#add_specimens(*specimens_and_params) ⇒ SpecimenCollectionGroup

Adds specimens to this protocol. The following parameter options are supported:

  • :participant - the Participant from whom the specimen is collected

  • :biospecimens - the collected top-level underived specimens

  • additional SCG parameters as described in SpecimenCollectionGroup#merge.

If the options does not include a :collection_protocol_event, then the SCG is assigned to the first collection event in this protocol. If the options does not include a :specimen_collection_site, then the SCG is assigned to the participant’s collection site as determined by Participant#collection_site, if that can be uniquely determined.

This add_specimens method adds the following parameter options before calling the SpecimenCollectionGroup constructor:

  • :registration => a new CollectionProtocolRegistration for this protocol and the specified participant

If there is no :name parameter, then this method builds a new unique SCG name as this CollectionProtocol’s name followed by a unique suffix.

Parameters:

  • specimens_and_params ((<Specimen>, {Symbol => Object})) —

    the specimens to add followed by the required parameter hash

Returns:

Raises:



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# File 'lib/catissue/domain/collection_protocol.rb', line 101

def add_specimens(*specimens_and_params)
  params = specimens_and_params.pop
  spcs = specimens_and_params
  # validate arguments
  unless params then
    raise ArgumentError.new("Collection parameters are missing when adding specimens to protocol #{self}")
  end
  # there must be a participant
  pnt = params.delete(:participant)
  unless pnt then
    raise ArgumentError.new("Participant missing from collection parameters: #{params.qp}")
  end
  # there must be a receiver
  unless params[:receiver] then
    raise ArgumentError.new("Receiver missing from collection parameters: #{params.qp}")
  end
  # the required registration
  params[:registration] ||= registration(pnt) || make_cpr(pnt)
  # the new SCG
  scg = SpecimenCollectionGroup.new(params)
  # set each Specimen SCG
  spcs.each { |spc| spc.specimen_collection_group = scg }
  scg
end

#consent_tiers ⇒ Java::JavaUtil::Set

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

Returns:

  • (Java::JavaUtil::Set) —

    the tiers



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# File 'lib/catissue/domain/collection_protocol.rb', line 16

def consent_tiers
  getConsentTierCollection or (self.consent_tiers = Java::JavaUtil::LinkedHashSet.new)
end

#default_site ⇒ CaTissue::Site?

Returns the default protocol site, determined as follows:

  • If there is exactly one authorized site for this protocol, then that is the default site.

  • If there is exactly two authorized sites for this protocol, then the site other than the Site.default_site is returned.

  • Otherwise, this method returns nil.

Returns:



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# File 'lib/catissue/domain/collection_protocol.rb', line 133

def default_site
 case sites.size
  when 1 then sites.first
  when 2 then sites.select { |site| site.name != CaTissue::Site.default_site.name }
  end
end

#first_event ⇒ Object

Returns the event in this protocol with the earliest study calendar event point.



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# File 'lib/catissue/domain/collection_protocol.rb', line 68

def first_event
  events.sort_by { |event| event.event_point or CollectionProtocolEvent::DEFAULT_EVENT_POINT }.first
end

#participants ⇒ Object

Returns all participants registered in this protocol.



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# File 'lib/catissue/domain/collection_protocol.rb', line 52

def participants
  registrations.nil? ? [] : registrations.map { |reg| reg.participant }
end

#register(participant, ppi = nil) ⇒ Object

Returns a new CollectionProtocolRegistration for the specified participant in this CollectionProtocol with optional protocol_participant_identifier ppi.



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# File 'lib/catissue/domain/collection_protocol.rb', line 58

def register(participant, ppi=nil)
  CollectionProtocolRegistration.new(:participant => participant, :protocol => self, :protocol_participant_identifier => ppi)
end

#registration(participant) ⇒ Object

Returns the CollectionProtocolRegistration for the specified participant in this CollectionProtocol,



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# File 'lib/catissue/domain/collection_protocol.rb', line 63

def registration(participant)
  registrations.detect { |registration| registration.participant == participant }
end

#specimens(participant = nil) ⇒ Object

Returns the specimens collected from the given participant for this CollectionProtocol, or all specimens in this protocol if participant is nil.



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# File 'lib/catissue/domain/collection_protocol.rb', line 74

def specimens(participant=nil)
  if participant.nil? then return registrations.map { |reg| reg.specimens }.flatten end
  reg = registration(participant)
  reg.nil? ? Array::EMPTY_ARRAY : reg.specimens
end

#uniquify ⇒ Object

Makes this CP’s short and long title unique.



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# File 'lib/catissue/domain/uniquify.rb', line 8

def uniquify
  super
  self.title = short_title
end