ccls-ccls_engine 3.11.0

data/app/models/address.rb

@@ -0,0 +1,70 @@
+#	Address for a study_subject
+#	Actually, this may be used for things other than subjects
+class Address < ActiveRecordShared
+
+	default_scope :order => 'created_at DESC'
+
+	has_many :interviews
+	has_one :addressing
+	has_one :study_subject, :through => :addressing
+	belongs_to :address_type
+
+	validate :address_type_matches_line
+
+	validates_presence_of :address_type_id
+	validates_presence_of :address_type, :if => :address_type_id
+
+	validates_presence_of :line_1
+	validates_length_of   :line_1, :maximum => 250, :allow_blank => true
+	validates_length_of   :line_2, :maximum => 250, :allow_blank => true
+	validates_length_of   :unit,   :maximum => 250, :allow_blank => true
+	validates_presence_of :city
+	validates_length_of   :city,   :maximum => 250, :allow_blank => true
+	validates_presence_of :state
+	validates_length_of   :state,  :maximum => 250, :allow_blank => true
+	validates_presence_of :zip
+	validates_length_of   :zip, :maximum => 10, :allow_blank => true
+
+	#	this needs to be unique, but is only used during importing
+	validates_uniqueness_of :external_address_id, :allow_blank => true
+
+	validates_format_of :zip,
+		:with => /\A\s*\d{5}(-)?(\d{4})?\s*\z/,
+		:message => "should be 12345, 123451234 or 12345-1234", :allow_blank => true
+
+	# Would it be better to do this before_validation?
+	before_save :format_zip, :if => :zip_changed?
+
+	#	Returns a string with the city, state and zip
+	def csz
+		"#{self.city}, #{self.state} #{self.zip}"
+	end
+
+protected
+
+	#	Determine if the address is a PO Box and then
+	#	require that the address type NOT be a residence.
+	def address_type_matches_line
+		#	It is inevitable that this will match too much
+		#	Pobox Street?
+		if(( line_1 =~ /p.*o.*box/i ) &&
+			( address_type_id.to_s == '1' ))	#	1 is 'residence'
+			errors.add(:address_type_id,
+				"must not be residence with PO Box") 
+		end
+	end
+
+	#	Simply squish the zip removing leading and trailing spaces.
+	#	zip MUST be a string or this won't work. Will always be
+	#	a string when sent from a form.
+	def format_zip
+		#	zip was nil during import and skipping validations
+		self.zip.squish! unless zip.nil?
+		#	convert to 12345-1234
+		if !self.zip.nil? and self.zip.length > 5
+			old = self.zip.gsub(/\D/,'')
+			self.zip = "#{old[0..4]}-#{old[5..8]}"
+		end
+	end
+
+end

data/app/models/address_type.rb

@@ -0,0 +1,15 @@
+#	The type of address (home,work,residence,pobox,etc.)
+class AddressType < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+	has_many :addresses
+
+	#	Returns the key
+	def to_s
+		self.key
+	end
+
+end

data/app/models/addressing.rb

@@ -0,0 +1,147 @@
+#	Rich join of Subject and Address
+class Addressing < ActiveRecordShared
+
+	belongs_to :study_subject
+	belongs_to :address
+	belongs_to :data_source
+
+	#	TODO test this.  Also may not need current_user now.
+#	This works in the console and such, but ActiveScaffold tries
+#	to use it in a join, but it is in a different database so fails.
+#	May be able to make it work in AS, but need to fiddle.
+#	belongs_to :verified_by, :foreign_key => 'verified_by_uid',
+#		:class_name => 'User', :primary_key => 'uid'
+
+	delegate :is_other?, :to => :data_source, :allow_nil => true, :prefix => true
+	delegate :address_type, :address_type_id,
+		:line_1,:line_2,:unit,:city,:state,:zip,:csz,:county,
+		:to => :address, :allow_nil => true
+
+	attr_accessor :current_user
+
+	#	flag used in study_subject's nested attributes for addressing
+	#		to not reject if address fields are blank.
+	attr_accessor :address_required
+
+	validates_length_of   :why_invalid,  :maximum => 250, :allow_blank => true
+	validates_presence_of :why_invalid,  :if => :is_not_valid?
+	validates_length_of   :how_verified, :maximum => 250, :allow_blank => true
+	validates_presence_of :how_verified, :if => :is_verified?
+	validates_complete_date_for :valid_from, :allow_nil => true
+	validates_complete_date_for :valid_to,   :allow_nil => true
+
+	validates_presence_of :data_source_other, :if => :data_source_is_other?
+
+
+
+
+	attr_protected :study_subject_id, :study_subject
+
+
+
+
+	validates_inclusion_of :current_address, :is_valid,
+		:address_at_diagnosis,
+			:in => YNDK.valid_values, :allow_nil => true
+
+
+	named_scope :current, :conditions => [
+		'current_address IS NOT NULL AND current_address != 2'
+	]
+
+	named_scope :historic, :conditions => [
+		'current_address IS NULL OR current_address = 2'
+	]
+
+	#	Don't do the rejections here.
+	accepts_nested_attributes_for :address
+
+	attr_accessor :subject_moved
+
+	after_save :create_subject_moved_event, :if => :subject_moved
+
+	before_save :set_verifier, 
+		:if => :is_verified?, 
+		:unless => :is_verified_was
+
+	before_save :nullify_verifier, 
+		:unless => :is_verified?,
+		:if => :is_verified_was
+
+	after_create :check_state_for_eligibilty
+
+	#	Returns boolean of comparison of is_valid == 2 or 999
+	#	Rails SHOULD convert incoming string params to integer.
+	def is_not_valid?
+#		[2,999].include?(is_valid.to_i)
+		[2,999].include?(is_valid)
+	end
+
+protected
+
+	#	Set verified time and user if given
+	def set_verifier
+		self.verified_on = Time.now
+		self.verified_by_uid = current_user.try(:uid)||''
+	end
+
+	#	Unset verified time and user
+	def nullify_verifier
+		self.verified_on = nil
+		self.verified_by_uid = nil
+	end
+
+	def check_state_for_eligibilty
+		if( state != 'CA' && study_subject && 
+			( hxe = study_subject.enrollments.find_by_project_id(Project['HomeExposures'].id) ) &&
+			address_type == AddressType['residence'] )
+
+			#	This is an after_save so using 1 NOT 0
+			ineligible_reason = if( study_subject.residence_addresses_count == 1 )
+				IneligibleReason['newnonCA']
+			else
+				IneligibleReason['moved']
+			end
+
+			hxe.update_attributes(
+				:is_eligible => YNDK[:no],
+				:ineligible_reason => ineligible_reason
+			)
+
+			oet = OperationalEventType['ineligible']
+			if( oet.blank? )
+				errors.add(:base,"OperationalEventType['ineligible'] not found")
+				raise ActiveRecord::RecordNotSaved
+			end
+
+			OperationalEvent.create!(
+				:enrollment => hxe,
+				:operational_event_type => oet,
+				:occurred_on => Date.today,
+				:description => ineligible_reason.to_s
+			)
+
+		end
+	end
+
+	#	this will actually create an event on creation as well
+	#	if attributes match
+	def create_subject_moved_event
+		#	subject_moved will most likely be a string 'true' or 'false'
+		#		as it will really only come as a hash value from a view.
+		#	.true? is a common_lib#object method.
+		if subject_moved.true? &&
+				current_address == YNDK[:no] &&
+				current_address_was != YNDK[:no] &&
+				address.address_type == AddressType['residence']
+			ccls_enrollment = study_subject.enrollments.find_or_create_by_project_id(
+				Project['ccls'].id)
+			OperationalEvent.create!(
+				:enrollment => ccls_enrollment,
+				:operational_event_type => OperationalEventType['subject_moved'],
+				:occurred_on            => Date.today
+			)
+		end
+	end
+
+end

data/app/models/aliquot.rb

@@ -0,0 +1,44 @@
+#	==	requires
+#	*	sample_id
+#	*	unit_id
+#	*	owner_id
+class Aliquot < ActiveRecordShared
+
+	belongs_to :sample
+	belongs_to :unit
+	belongs_to :aliquot_sample_format
+	belongs_to :owner, :class_name => "Organization"
+	has_many :transfers
+
+	validates_presence_of :sample
+	validates_presence_of :unit
+	validates_presence_of :owner
+	validates_length_of   :location, :maximum => 250, :allow_blank => true
+	validates_length_of   :mass,     :maximum => 250, :allow_blank => true
+
+	#	Create a #Transfer for the given #Aliquot from the 
+	#	current owner(#Organization) to the given #Organization.
+	def transfer_to(organization)
+		org = Organization.find(organization)
+		#	I don't think that the transaction is necessary
+		#	but I also don't think that it will hurt.
+		Aliquot.transaction do
+			#	wrap this in a transaction because
+			#	we don't want the aliquot.owner being
+			#	out of sync with the last transfer.to
+			self.transfer.to(org).save!
+		end
+	end
+
+protected
+
+	#	Begin building the #Transfer from the current
+	#	owner(#Organization)
+	def transfer
+		Transfer.new({
+			:aliquot_id => self.id,
+			:from_organization_id => self.owner_id
+		})
+	end
+
+end

data/app/models/aliquot_sample_format.rb

@@ -0,0 +1,13 @@
+#	==	requires
+#	*	description (unique and >3 chars)
+class AliquotSampleFormat < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :aliquots
+	has_many :samples
+
+end

data/app/models/analysis.rb

@@ -0,0 +1,14 @@
+# don't know exactly
+class Analysis < ActiveRecordShared
+#
+#	TODO remove the habtm and replace it with hmt SubjectAnalyses ?
+#
+	has_and_belongs_to_many :study_subjects
+
+	belongs_to :analyst, :class_name => 'Person'
+	belongs_to :analytic_file_creator, :class_name => 'Person'
+	belongs_to :project
+
+	acts_like_a_hash
+
+end

data/app/models/bc_request.rb

@@ -0,0 +1,20 @@
+class BcRequest < ActiveRecordShared
+
+	belongs_to     :study_subject
+	attr_protected :study_subject_id, :study_subject
+
+	validates_length_of :request_type, :maximum => 250, :allow_blank => true
+	validates_length_of :status,       :maximum => 250, :allow_blank => true
+	validates_length_of :notes,        :maximum => 65000, :allow_blank => true
+
+#	validates_inclusion_of :status, :in => statuses
+
+	def self.statuses
+		%w( active waitlist pending complete )
+	end
+
+	def to_s
+		( study_subject ) ? study_subject.studyid : self
+	end
+
+end

data/app/models/candidate_control.rb

@@ -0,0 +1,101 @@
+class CandidateControl < ActiveRecordShared
+
+	belongs_to :study_subject
+	attr_protected :study_subject_id, :study_subject
+
+	validates_presence_of  :first_name
+	validates_presence_of  :last_name
+	validates_presence_of  :dob
+	validates_inclusion_of :reject_candidate, :in => [true, false]
+	validates_presence_of  :rejection_reason, :if => :reject_candidate
+	validates_length_of    :related_patid, :is => 4, :allow_blank => true
+	validates_length_of    :state_registrar_no, :maximum => 25, :allow_blank => true
+	validates_length_of    :local_registrar_no, :maximum => 25, :allow_blank => true
+
+	validates_length_of    :first_name, :middle_name, :last_name,
+		:birth_county, :birth_type, :mother_maiden_name,
+		:rejection_reason, :maximum => 250, :allow_blank => true
+
+#	validates_inclusion_of :sex, :in => %w( M F DK )
+	validates_inclusion_of :sex, :in => valid_sex_values
+
+
+	validates_inclusion_of :mother_hispanicity_id, :father_hispanicity_id,
+			:in => YNODK.valid_values, :allow_nil => true
+	validates_inclusion_of :mom_is_biomom, :dad_is_biodad,
+			:in => YNDK.valid_values, :allow_nil => true
+
+
+	#	Returns string containing candidates's first, middle and last name
+	def full_name
+		[first_name, middle_name, last_name].delete_if(&:blank?).join(' ')
+	end
+
+	#	Returns string containing candidates's mother's first, middle and last name
+	def mother_full_name
+		[mother_first_name, mother_middle_name, mother_last_name].delete_if(&:blank?).join(' ')
+	end
+
+	def create_study_subjects(case_subject,grouping = '6')
+		next_orderno = case_subject.next_control_orderno(grouping)
+
+		CandidateControl.transaction do
+
+			#	Use a block so can assign all attributes without concern for attr_protected
+			child = StudySubject.new do |s|
+				s.subject_type = SubjectType['Control']
+				s.vital_status = VitalStatus['living']
+				s.sex                   = sex
+				s.mom_is_biomom         = mom_is_biomom
+				s.dad_is_biodad         = dad_is_biodad
+				s.mother_hispanicity_id = mother_hispanicity_id
+				s.father_hispanicity_id = father_hispanicity_id
+				s.birth_type            = birth_type
+				s.mother_yrs_educ       = mother_yrs_educ
+				s.father_yrs_educ       = father_yrs_educ
+				s.birth_county          = birth_county
+				s.hispanicity_id        = ( 
+					( [mother_hispanicity_id,father_hispanicity_id].include?(1) ) ? 1 : nil )
+				s.first_name         = first_name
+				s.middle_name        = middle_name
+				s.last_name          = last_name
+				s.dob                = dob
+				s.mother_first_name  = mother_first_name
+				s.mother_middle_name = mother_middle_name
+				s.mother_last_name   = mother_last_name
+				s.mother_maiden_name = mother_maiden_name
+				s.mother_race_id     = mother_race_id
+				s.father_race_id     = father_race_id
+
+				s.case_control_type  = grouping
+				s.state_registrar_no = state_registrar_no
+				s.local_registrar_no = local_registrar_no
+				s.orderno            = next_orderno
+				s.matchingid         = case_subject.subjectid
+				s.patid              = case_subject.patid
+				s.is_matched         = true
+			end
+			child.save!
+			child.assign_icf_master_id
+
+
+#	TODO May have to set is_matched for both the Case and Control here [#217]
+#	We will default it to null and add logic to set it to true for both the new control and their related case when a new control is added to study_subjects from candidate_controls.
+			case_subject.update_attributes!(:is_matched => true)
+
+
+			#	NOTE this may require passing info
+			#	that is in the candidate_control record, but not in the child subject
+			#		mother_hispanicity_id	(actually this is now)
+			#	worst case scenario is just create the full mother here
+			#	rather than through the child.
+			child.create_mother	#	({ .... })
+	
+			self.study_subject_id = child.id
+			self.assigned_on = Date.today
+			self.save!
+		end
+		self
+	end
+
+end

data/app/models/context.rb

@@ -0,0 +1,23 @@
+#	==	requires
+#	*	description (unique and >3 chars)
+class Context < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :units
+#	has_many :people
+
+	has_many :context_data_sources
+	has_many :data_sources, :through => :context_data_sources
+
+	validates_length_of :notes, :maximum => 65000, :allow_blank => true
+
+	#	Returns description
+	def to_s
+		description
+	end
+
+end