ccls-ccls_engine 3.11.0

data/app/models/section.rb

@@ -0,0 +1,18 @@
+#	==	requires
+#	*	key ( unique )
+#	*	description ( > 3 chars )
+class Section < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :follow_ups
+
+	#	Returns description
+	def to_s
+		description
+	end
+
+end

data/app/models/state.rb

@@ -0,0 +1,25 @@
+# Currently just US states + DC
+class State < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+
+	validates_presence_of   :code
+	validates_presence_of   :name
+	validates_presence_of   :fips_state_code
+	validates_presence_of   :fips_country_code
+	validates_uniqueness_of :code
+	validates_uniqueness_of :name
+	validates_uniqueness_of :fips_state_code
+	validates_length_of     :code, :maximum => 250, :allow_blank => true
+	validates_length_of     :name, :maximum => 250, :allow_blank => true
+	validates_length_of     :fips_state_code, :maximum => 250, :allow_blank => true
+	validates_length_of     :fips_country_code, :maximum => 250, :allow_blank => true
+
+	# Returns an array of state abbreviations.
+	def self.abbreviations
+		@@abbreviations ||= all.collect(&:code)
+	end
+
+end

data/app/models/study_subject.rb

@@ -0,0 +1,237 @@
+#	==	requires
+#	*	subject_type_id
+class StudySubject < ActiveRecordShared
+
+	class NotTwoAbstracts < StandardError; end
+	class DuplicatesFound < StandardError; end
+
+	#	This is purely an attempt at organization.
+	#	Initially, this was by purpose, but now modifying to
+	#	be by association or topic as this seems more logical.
+	#	Also trying to map this same organization in the tests
+	#	so that autotest triggers the more likely effected tests.
+	include StudySubjectAssociations
+	include StudySubjectValidations
+
+	include StudySubjectPatient
+	include StudySubjectPii
+	include StudySubjectIdentifier
+	include StudySubjectDuplicates
+	include StudySubjectAbstracts
+	include StudySubjectRaces
+	include StudySubjectLanguages
+	include StudySubjectAddresses
+
+	#	Declaration order matters. 
+	#	OperationalEvents are through Enrollments.
+	include StudySubjectEnrollments
+	include StudySubjectOperationalEvents
+
+	include StudySubjectHomexOutcome
+	include StudySubjectInterviews
+
+	delegate :is_other?, :to => :guardian_relationship, 
+		:allow_nil => true, :prefix => true 
+
+	#	can lead to multiple piis in db for study_subject
+	#	if not done correctly
+	#	s.update_attributes({"pii_attributes" => { "ssn" => "123456789", 'state_id_no' => 'x'}})
+	#	s.update_attributes({"pii_attributes" => { "ssn" => "987654321", 'state_id_no' => 'a'}})
+	#	Pii.find(:all, :conditions => {:study_subject_id => s.id }).count 
+	#	=> 2
+	#	without the :id attribute, it will create, but NOT destroy
+	#	s.reload.pii  will return the first one (sorts by id)
+	#	s.pii.destroy will destroy the last one !?!?!?
+	#	Make all these require a unique study_subject_id
+	#	Newer versions of rails actually nullify the old record
+
+	accepts_nested_attributes_for :phone_numbers,
+		:reject_if => proc { |attrs| attrs[:phone_number].blank? }
+	accepts_nested_attributes_for :gift_cards
+
+	#	Find the case or control subject with matching familyid except self.
+	def child
+		if (subject_type_id == self.class.subject_type_mother_id) && !familyid.blank?
+			self.class.find(:first,
+				:include => [:subject_type],
+				:conditions => [
+					"study_subjects.id != ? AND subjectid = ? AND subject_type_id IN (?)", 
+						id, familyid, 
+						[self.class.subject_type_case_id,self.class.subject_type_control_id] ]
+			)
+		else
+			nil
+		end
+	end
+
+	#	Find the subject with matching familyid and subject_type of Mother.
+	def mother
+		return nil if familyid.blank?
+		self.class.find(:first,
+			:include => [:subject_type],
+			:conditions => { 
+				:familyid        => familyid,
+				:subject_type_id => self.class.subject_type_mother_id
+			}
+		)
+	end
+
+	#	Find all the subjects with matching familyid except self.
+	def family
+		return [] if familyid.blank?
+		self.class.find(:all,
+			:include => [:subject_type],
+			:conditions => [
+				"study_subjects.id != ? AND familyid = ?", id, familyid ]
+		)
+	end
+
+	#	Find all the subjects with matching matchingid except self.
+	def matching
+		return [] if matchingid.blank?
+		self.class.find(:all,
+			:include => [:subject_type],
+			:conditions => [
+				"study_subjects.id != ? AND matchingid = ?", 
+					id, matchingid ]
+		)
+	end
+
+	#	Find all the subjects with matching patid with subject_type Control except self.
+	#	If patid is nil, this sql doesn't work.  
+	#			TODO Could fix, but this situation is unlikely.
+	def controls
+		return [] unless is_case?
+		self.class.find(:all, 
+			:include => [:subject_type],
+			:conditions => [
+				"study_subjects.id != ? AND patid = ? AND subject_type_id = ?", 
+					id, patid, self.class.subject_type_control_id ] 
+		)
+	end
+
+	def rejected_controls
+		return [] unless is_case?
+		CandidateControl.find(:all,
+			:conditions => {
+				:related_patid    => patid,
+				:reject_candidate => true
+			}
+		)
+	end
+
+	def to_s
+		[childid,'(',studyid,full_name,')'].compact.join(' ')
+	end
+
+	#	Returns boolean of comparison
+	#	true only if type is Case
+	def is_case?
+		subject_type_id == self.class.subject_type_case_id
+	end
+
+	#	Returns boolean of comparison
+	#	true only if type is Control
+	def is_control?
+		subject_type_id == self.class.subject_type_control_id
+	end
+
+	#	Returns boolean of comparison
+	#	true only if type is Mother
+	def is_mother?
+		subject_type_id == self.class.subject_type_mother_id
+	end
+
+	def self.search(params={})
+		StudySubjectSearch.new(params).study_subjects
+	end
+
+	#	Create (or just return mother) a mother subject based on subject's own data.
+	def create_mother
+		return self if is_mother?
+		#	The mother method will effectively find and itself.
+		existing_mother = mother
+		if existing_mother
+			existing_mother
+		else
+			new_mother = self.class.new do |s|
+				s.subject_type_id = self.class.subject_type_mother_id
+				s.vital_status_id = VitalStatus['living'].id
+				s.sex = 'F'
+				s.hispanicity_id = mother_hispanicity_id
+				s.first_name  = mother_first_name
+				s.middle_name = mother_middle_name
+				s.last_name   = mother_last_name
+				s.maiden_name = mother_maiden_name
+
+				#	protected attributes!
+				s.matchingid = matchingid
+				s.familyid   = familyid
+			end
+			new_mother.save!
+			new_mother.assign_icf_master_id
+			new_mother
+		end
+	end
+
+	def assign_icf_master_id
+		if icf_master_id.blank?
+			next_icf_master_id = IcfMasterId.next_unused
+			if next_icf_master_id
+				self.update_attribute(:icf_master_id, next_icf_master_id.to_s)
+				next_icf_master_id.study_subject = self
+				next_icf_master_id.assigned_on   = Date.today
+				next_icf_master_id.save!
+			end
+		end
+		self
+	end
+
+	def next_control_orderno(grouping='6')
+		return nil unless is_case?
+		last_control = self.class.find(:first, 
+			:order => 'orderno DESC', 
+			:conditions => { 
+				:subject_type_id   => self.class.subject_type_control_id,
+				:case_control_type => grouping,
+				:matchingid        => self.subjectid
+			}
+		)
+		( last_control.try(:orderno) || 0 ) + 1
+	end
+
+	def self.find_case_by_patid(patid)
+		self.find(:first,	#	patid is unique so better only be 1
+			:conditions => [
+				'subject_type_id = ? AND patid = ?',
+				subject_type_case_id, patid
+			]
+		)
+	end
+
+	def icf_master_id_to_s
+		( icf_master_id.blank? ) ?  "[no ID assigned]" : icf_master_id
+	end
+
+	def childid_to_s
+		( is_mother? ) ? "#{child.try(:childid)} (mother)" : childid
+	end
+
+	def studyid_to_s
+		( is_mother? ) ? "n/a" : studyid
+	end
+
+protected
+
+	#	Use these to stop the constant checking.
+	def self.subject_type_mother_id
+		@@subject_type_mother_id ||= SubjectType['Mother'].id
+	end
+	def self.subject_type_control_id
+		@@subject_type_control_id ||= SubjectType['Control'].id
+	end
+	def self.subject_type_case_id
+		@@subject_type_case_id ||= SubjectType['Case'].id
+	end
+
+end

data/app/models/study_subject_abstracts.rb

@@ -0,0 +1,47 @@
+#
+#	Simply extracted some code to clean up model.
+#	I'd like to do this to all of the really big classes
+#	but let's see how this goes first.
+#
+module StudySubjectAbstracts
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+#	Hmm?  How to do this here?
+#	class NotTwoAbstracts < StandardError; end
+
+	has_many :abstracts
+	has_one :first_abstract, :class_name => 'Abstract',
+		:conditions => [
+			"entry_1_by_uid IS NOT NULL AND " <<
+			"entry_2_by_uid IS NULL AND " <<
+			"merged_by_uid  IS NULL" ]
+	has_one :second_abstract, :class_name => 'Abstract',
+		:conditions => [
+			"entry_2_by_uid IS NOT NULL AND " <<
+			"merged_by_uid  IS NULL" ]
+	has_one :merged_abstract, :class_name => 'Abstract',
+		:conditions => [ "merged_by_uid IS NOT NULL" ]
+	has_many :unmerged_abstracts, :class_name => 'Abstract',
+		:conditions => [ "merged_by_uid IS NULL" ]
+
+	def abstracts_the_same?
+		raise StudySubject::NotTwoAbstracts unless abstracts_count == 2
+		#	abstracts.inject(:is_the_same_as?) was nice
+		#	but using inject is ruby >= 1.8.7
+		return abstracts[0].is_the_same_as?(abstracts[1])
+	end
+
+	def abstract_diffs
+		raise StudySubject::NotTwoAbstracts unless abstracts_count == 2
+		#	abstracts.inject(:diff) was nice
+		#	but using inject is ruby >= 1.8.7
+		return abstracts[0].diff(abstracts[1])
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectAbstracts
+__END__

data/app/models/study_subject_addresses.rb

@@ -0,0 +1,34 @@
+#
+#	Simply extracted some code to clean up model.
+#	I'd like to do this to all of the really big classes
+#	but let's see how this goes first.
+#
+module StudySubjectAddresses
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+	has_many :addressings
+	has_many :addresses, :through => :addressings
+
+	accepts_nested_attributes_for :addressings,
+		:reject_if => proc { |attrs|
+			!attrs[:address_required] &&
+			attrs[:address_attributes][:line_1].blank? &&
+			attrs[:address_attributes][:line_2].blank? &&
+			attrs[:address_attributes][:unit].blank? &&
+			attrs[:address_attributes][:city].blank? &&
+			attrs[:address_attributes][:zip].blank? &&
+			attrs[:address_attributes][:county].blank?
+		}
+
+	#	Returns number of addresses with 
+	#	address_type.key == 'residence'
+	def residence_addresses_count
+		addresses.count(:conditions => { :address_type_id => AddressType['residence'].id })
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectAddresses

data/app/models/study_subject_associations.rb

@@ -0,0 +1,38 @@
+#
+#	Simply extracted some code to clean up model.
+#	I'd like to do this to all of the really big classes
+#	but let's see how this goes first.
+#
+module StudySubjectAssociations
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+	belongs_to :subject_type
+	belongs_to :vital_status
+
+	has_and_belongs_to_many :analyses
+	has_many :gift_cards
+	has_many :phone_numbers
+	has_many :samples
+	has_one :home_exposure_response
+	has_many :bc_requests
+	belongs_to :guardian_relationship, :class_name => 'SubjectRelationship'
+
+##########
+#
+#	Declaration order does matter.  Because of a patient callback that 
+#	references the study_subject's dob when using nested attributes, 
+#	pii NEEDS to be BEFORE patient.
+#
+#	identifier should also be before patient
+#
+#	has_one :identifier
+#	has_one :pii
+#
+##########
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectAssociations

data/app/models/study_subject_duplicates.rb

@@ -0,0 +1,111 @@
+#
+#	Simply extracted some code to clean up model.
+#	I'd like to do this to all of the really big classes
+#	but let's see how this goes first.
+#
+module StudySubjectDuplicates
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+	#
+	#	Basically this is just a custom search expecting only the 
+	#	following possible params for search / comparison ...
+	#
+	#		mother_maiden_name
+	#		hospital_no
+	#		dob
+	#		sex
+	#		admit_date
+	#		organization_id
+	#
+	#		Would want to explicitly exclude self, but this check is
+	#		to be done BEFORE subject creation so won't actually
+	#		have an id to use to exclude itself anyway.
+	#
+	#		For adding controls, will need to be able to exclude case
+	#		so adding :exclude_id option somehow
+	#
+	def self.duplicates(params={})
+		conditions = [[],{}]
+
+		if params.has_key?(:hospital_no) and !params[:hospital_no].blank?
+			conditions[0] << '(hospital_no = :hospital_no)'
+			conditions[1][:hospital_no] = params[:hospital_no]
+		end
+
+		#	This is effectively the only test for adding controls
+		#	as the other attributes are from the patient model
+		#	which is only for cases.
+		if params.has_key?(:dob) and !params[:dob].blank? and
+				params.has_key?(:sex) and !params[:sex].blank? and 
+				params.has_key?(:mother_maiden_name)
+#	since remove nullify of name fields, added comparison to ""
+			conditions[0] << '(dob = :dob AND sex = :sex AND ( mother_maiden_name IS NULL OR mother_maiden_name = "" OR mother_maiden_name = :mother_maiden_name ))'
+			conditions[1][:dob] = params[:dob]
+			conditions[1][:sex] = params[:sex]
+			#	added to_s as may be null so sql is valid and has '' rather than a blank
+			conditions[1][:mother_maiden_name] = params[:mother_maiden_name].to_s		
+		end
+		if params.has_key?(:admit_date) and !params[:admit_date].blank? and
+				params.has_key?(:organization_id) and !params[:organization_id].blank?
+			conditions[0] << '(admit_date = :admit AND organization_id = :org)'
+			conditions[1][:admit] = params[:admit_date]
+			conditions[1][:org] = params[:organization_id]
+		end
+
+		unless conditions[0].blank?
+			conditions_array = [ "(#{conditions[0].join(' OR ')})" ]
+			if params.has_key?(:exclude_id)
+				conditions_array[0] << " AND study_subjects.id != :exclude_id"
+				conditions[1][:exclude_id] = params[:exclude_id]
+			end
+			conditions_array << conditions[1]
+#puts conditions_array.inspect
+#["((hospital_no = :hospital_no) OR (dob = :dob AND sex = :sex AND ( mother_maiden_name IS NULL OR mother_maiden_name = :mother_maiden_name )) OR (admit_date = :admit AND organization_id = :org)) AND study_subjects.id != :exclude_id", {:hospital_no=>"matchthis", :org=>31, :admit=>Wed, 16 Nov 2011, :sex=>"F", :exclude_id=>3, :mother_maiden_name=>"", :dob=>Wed, 16 Nov 2011}]
+
+			find(:all,
+				#	have to do a LEFT JOIN, not the default INNER JOIN, here
+				#			:joins => [:pii,:patient,:identifier]
+				#	otherwise would only include subjects with pii, patient and identifier,
+				#	which would effectively exclude controls. (maybe that's ok?. NOT OK.)
+				:joins => [
+					'LEFT JOIN patients ON study_subjects.id = patients.study_subject_id'
+				],
+				:conditions => conditions_array
+			) 
+		else
+			[]
+		end
+	end
+
+	def duplicates(options={})
+		self.class.duplicates({
+			:mother_maiden_name => self.mother_maiden_name,
+			:hospital_no => self.hospital_no,
+			:dob => self.dob,
+			:sex => self.sex,
+			:admit_date => self.admit_date,
+			:organization_id => self.organization_id
+		}.merge(options))
+	end
+
+	def raf_duplicate_creation_attempted(attempted_subject)
+		ccls_enrollment = enrollments.find_or_create_by_project_id(Project['ccls'].id)
+		OperationalEvent.create!(
+			:enrollment => ccls_enrollment,
+			:operational_event_type => OperationalEventType['DuplicateCase'],
+			:occurred_on            => Date.today,
+			:description            => "a new RAF for this subject was submitted by " <<
+				"#{attempted_subject.admitting_oncologist} of " <<
+				"#{attempted_subject.organization} " <<
+				"with hospital number: " <<
+				"#{attempted_subject.hospital_no}."
+		)
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectDuplicates
+__END__