ccls-ccls_engine 3.11.0

data/app/models/study_subject_pii.rb

@@ -0,0 +1,74 @@
+#
+#	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 StudySubjectPii
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+	#	TODO include maiden_name just in case is mother???
+	def childs_names
+		[first_name, middle_name, last_name ]
+	end
+
+	#	Returns string containing study_subject's first, middle and last initials
+	def initials
+		childs_names.delete_if(&:blank?).collect{|s|s.chars.first}.join()
+	end
+
+	#	Returns string containing study_subject's first, middle and last name
+	#	Use delete_if(&:blank?) instead of compact, which only removes nils.
+	def full_name
+		fullname = childs_names.delete_if(&:blank?).join(' ')
+		( fullname.blank? ) ? '[name not available]' : fullname
+	end
+
+	def fathers_names
+		[father_first_name, father_middle_name, father_last_name ]
+	end
+
+	#	Returns string containing study_subject's father's first, middle and last name
+	def fathers_name
+		fathersname = fathers_names.delete_if(&:blank?).join(' ')
+		( fathersname.blank? ) ? '[name not available]' : fathersname
+	end
+
+	def mothers_names
+		[mother_first_name, mother_middle_name, mother_last_name ]
+	end
+
+	#	Returns string containing study_subject's mother's first, middle and last name
+	#	TODO what? no maiden name?
+	def mothers_name
+		mothersname = mothers_names.delete_if(&:blank?).join(' ')
+		( mothersname.blank? ) ? '[name not available]' : mothersname
+	end
+
+	def guardians_names
+		[guardian_first_name, guardian_middle_name, guardian_last_name ]
+	end
+
+	#	Returns string containing study_subject's guardian's first, middle and last name
+	def guardians_name
+		guardiansname = guardians_names.delete_if(&:blank?).join(' ')
+		( guardiansname.blank? ) ? '[name not available]' : guardiansname
+	end
+
+#
+#	TODO I hate this.  It is revolting.  More?  Yes, please.
+#
+	#	I don't know if I still need this
+	#	commented out 20101014
+	#	uncommented 20101014
+	def dob	#	overwrite default dob method for formatting
+		#	added to_date to fix sqlite3 quirk which doesn't	(why am I using sqlite3?)  old comment?
+		#	differentiate between times and dates.
+		read_attribute(:dob).try(:to_s,:dob).try(:to_date)
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectPii

data/app/models/study_subject_races.rb

@@ -0,0 +1,25 @@
+#
+#	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 StudySubjectRaces
+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 :subject_races
+	has_many :races, :through => :subject_races
+
+	accepts_nested_attributes_for :subject_races, 
+		:allow_destroy => true,
+		:reject_if => proc{|attributes| attributes['race_id'].blank? }
+
+	def race_names
+		races.collect(&:to_s).join(', ')
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectRaces

data/app/models/study_subject_search.rb

@@ -0,0 +1,260 @@
+# This has gotton out of control.  While it certainly still functions,
+#	I would advise that search commands be a bit more concise as most
+#	are only used in one location.
+class StudySubjectSearch < Search
+
+	self.searchable_attributes += [ :races, :types, :vital_statuses, :q,
+		:sample_outcome, :interview_outcome,
+		:projects, :has_gift_card, :patid,
+		:abstracts_count
+	]
+
+	self.attr_accessors += [ :search_gift_cards, :abstracts_count ]
+
+#	self.valid_orders.merge!({  #	NO!
+#	@valid_orders.merge!({      #	NO!
+	self.valid_orders = self.valid_orders.merge({
+		:id => 'study_subjects.id',	#	must remove any possible ambiguity
+		:childid => 'childid',
+		:last_name => 'last_name',
+		:first_name => 'first_name',
+		:dob => 'dob',
+		:studyid => 'patid',
+		:priority => 'recruitment_priority',
+		:sample_outcome => 'homex_outcomes.sample_outcome_id',
+		:sample_outcome_on => 'homex_outcomes.sample_outcome_on',
+		:patid => 'patid',
+		:abstracts_count => nil,
+		:interview_outcome_on => 'homex_outcomes.interview_outcome_on',
+		:sample_sent_on => nil,
+		:sample_received_on => nil,
+		:number => 'gift_cards.number',
+		:issued_on => 'gift_cards.issued_on'
+#
+#	TODO this isn't true no more.  gotta add another join
+#
+#		:sent_to_subject_on => 'samples.sent_to_subject_on',
+#		:received_by_ccls_at => 'samples.received_by_ccls_at'
+	})
+
+	def study_subjects
+		require_dependency 'gift_card.rb' unless GiftCard
+		@subjects ||= StudySubject.send(
+			(paginate?)?'paginate':'all',{
+				:select  => select,
+				:group   => group,
+				:having  => having,
+				:order   => search_order,
+				:joins   => joins,
+				:conditions => conditions
+			}.merge(
+				(paginate?)?{
+					:per_page => per_page||25,
+					:page     => page||1
+				}:{}
+			)
+		)
+	end
+	alias_method :subjects, :study_subjects
+
+private	#	THIS IS REQUIRED
+
+#	TODO as is not true
+#	I don't think that sorting by these fields is ever done.
+#	def samples_joins
+#		"JOIN samples ON study_subjects.id " <<
+#			"= samples.study_subject_id" if %w( sent_to_subject_on received_by_ccls_at ).include?(@order)
+#	end
+
+	def vital_statuses_joins
+		"INNER JOIN vital_statuses ON vital_statuses.id " <<
+			"= study_subjects.vital_status_id" unless vital_statuses.blank?
+	end
+
+	def vital_statuses_conditions
+		['vital_statuses.key IN (:vital_statuses)', { :vital_statuses => vital_statuses }
+			] unless vital_statuses.blank?
+	end
+
+	def patid_conditions
+		['patid = :patid', {:patid => patid}] unless patid.blank?
+	end
+
+
+	def races_joins
+#		"INNER JOIN races ON races.id = study_subjects.race_id" unless races.blank?
+		"LEFT JOIN subject_races ON study_subjects.id = subject_races.study_subject_id LEFT JOIN races ON races.id = subject_races.race_id" unless races.blank?
+	end
+
+#>> study_subjects = StudySubject.find(:all, :joins => "left join samples on study_subjects.id = samples.study_subject_id", :group => 'study_subjects.id', :having => ["sample_ids LIKE '%?%'",1], :select => "study_subjects.id, GROUP_CONCAT(samples.id) as sample_ids")
+#=> [#<StudySubject id: 1>, #<StudySubject id: 2014>]
+
+	def races_groups
+		'study_subjects.id' unless races.blank?
+	end
+	
+	def races_selects
+		"study_subjects.*, CONCAT('|',GROUP_CONCAT(races.description SEPARATOR '|'),'|') as race_descriptions" unless races.blank?
+	end
+
+	def races_havings
+		unless races.blank?
+			c = []
+			v = {}
+			races.each_with_index do |race,i|
+				c << "race_descriptions LIKE :r#{i}"
+				v["r#{i}".to_sym] = "%|#{race}|%"
+			end
+			[ c.join(' OR '), v ]
+		end
+	end
+
+
+	def types_joins
+		"INNER JOIN subject_types ON subject_types.id " <<
+			"= study_subjects.subject_type_id" unless types.blank?
+	end
+
+	def types_conditions
+		['subject_types.description IN (:types)', { :types => types }
+			] unless types.blank?
+	end
+
+	def gift_card_joins
+		#	A study_subject has many gift cards so this may pose a problem
+		"LEFT JOIN gift_cards ON gift_cards.study_subject_id = study_subjects.id" if( 
+			search_gift_cards || %w( number issued_on ).include?(@order))
+	end
+
+	def q_conditions
+		unless q.blank?
+			c = []
+			v = {}
+			q.to_s.split(/\s+/).each_with_index do |t,i|
+				c.push("first_name LIKE :t#{i}")
+				c.push("last_name LIKE :t#{i}")
+				c.push("patid LIKE :t#{i}")
+				c.push("childid LIKE :t#{i}")
+				c.push("gift_cards.number LIKE :t#{i}") if search_gift_cards
+				v["t#{i}".to_sym] = "%#{t}%"
+			end
+			[ "( #{c.join(' OR ')} )", v ]
+		end
+	end
+
+	def gift_card_conditions
+		unless has_gift_card.nil?
+			if has_gift_card
+				["gift_cards.id IS NOT NULL"]
+			else
+				["gift_cards.id IS NULL"]
+			end
+		end
+	end
+
+	#	join order matters and this MUST come before
+	#	those that join on home_outcomes!  Hmm?
+	#	How?  Added a sort to joins and an "a_" to this
+	def a_homex_outcome_joins
+		"LEFT JOIN homex_outcomes ON homex_outcomes.study_subject_id " <<
+			"= study_subjects.id" if( !sample_outcome.blank? ||
+				!interview_outcome.blank? ||
+				[ 'sample_outcome','sample_outcome_on','interview_outcome_on'].include?(@order) )
+	end
+
+	def sample_outcome_joins
+		"LEFT JOIN sample_outcomes ON sample_outcomes.id = " <<
+			"homex_outcomes.sample_outcome_id" unless
+				sample_outcome.blank?
+	end
+
+	def sample_outcome_conditions
+		unless sample_outcome.blank?
+			if sample_outcome =~ /^Complete$/i
+#				['sample_outcomes.key = :sample_outcome',{:sample_outcome => sample_outcome}]
+				['sample_outcomes.key IS NOT NULL && sample_outcomes.key NOT IN ("Sent","Pending")']
+			else
+				["(sample_outcomes.key != 'Complete' " <<
+						"OR sample_outcomes.key IS NULL)"]
+			end
+		end
+	end
+
+	def interview_outcome_joins
+		"LEFT JOIN interview_outcomes ON interview_outcomes.id = " <<
+			"homex_outcomes.interview_outcome_id" unless
+				interview_outcome.blank?
+	end
+
+	def interview_outcome_conditions
+		unless interview_outcome.blank?
+			if interview_outcome =~ /^Complete$/i
+				['interview_outcomes.key = :interview_outcome', {:interview_outcome => interview_outcome}]
+			else
+				["(interview_outcomes.key != 'Complete'" <<
+					"OR interview_outcomes.key IS NULL)"]
+			end
+		end
+	end
+
+	def projects_joins
+		unless projects.blank?
+			s = ''
+			projects.keys.each do |id|
+				s << "JOIN enrollments proj_#{id} ON study_subjects.id "<<
+						"= proj_#{id}.study_subject_id AND proj_#{id}.project_id = #{id} " 
+			end
+			s
+		end
+	end
+
+	def projects_conditions
+		unless projects.blank?
+			conditions = []
+			values = []
+			projects.each do |id,attributes|
+				attributes.each do |attr,val|
+					val = [val].flatten
+					if val.true_xor_false?
+						new_condition = case attr.to_s.downcase
+							when 'eligible'
+								"proj_#{id}.is_eligible " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'candidate'
+								"proj_#{id}.is_candidate " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'chosen'
+								"proj_#{id}.is_chosen " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'consented'
+								"proj_#{id}.consented " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'terminated'
+								"proj_#{id}.terminated_participation " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'closed'
+								"proj_#{id}.is_closed " <<
+									((val.true?)?'= 1':'!= 1')
+							when 'completed'
+								"proj_#{id}.completed_on IS " <<
+									((val.true?)?'NOT NULL':'NULL')
+						end	#	case attr.to_s.downcase
+						conditions << new_condition unless new_condition.blank?
+					end	#	if val.true_xor_false?
+				end	#	attributes.each
+			end #	projects.each
+			[conditions.compact,values].flatten(1) unless conditions.empty?
+		end #	unless projects.blank?
+	end	#	def projects_conditions
+
+	def abstracts_count_conditions
+		unless @abstracts_count.blank?
+			case @abstracts_count.to_s
+				when '0' then ["abstracts_count <= 0"]
+				when '1' then ["abstracts_count = 1"]
+				when '2' then ["abstracts_count = 2"]
+			end
+		end
+	end
+
+end

data/app/models/study_subject_validations.rb

@@ -0,0 +1,116 @@
+#
+#	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 StudySubjectValidations
+def self.included(base)
+#	Must delay the calls to these ActiveRecord methods
+#	or it will raise many "undefined method"s.
+base.class_eval do
+
+	validates_presence_of :subject_type_id
+	validates_presence_of :subject_type, :if => :subject_type_id
+
+	validate :presence_of_sex
+#	validates_inclusion_of :sex, :in => %w( M F DK ), :allow_blank => true
+	validates_inclusion_of :sex, :in => valid_sex_values, :allow_blank => true
+	validates_inclusion_of :do_not_contact, :in => [ true, false ]
+
+	validates_complete_date_for :reference_date, :allow_nil => true
+
+	validate :presence_of_dob, :unless => :is_mother?
+	validates_complete_date_for :dob, :allow_nil => true
+	validates_past_date_for     :dob, :allow_nil => true
+	validates_complete_date_for :died_on, :allow_nil => true
+	validates_uniqueness_of     :email, :icf_master_id, :state_id_no, 
+		:state_registrar_no, :local_registrar_no, :gbid, :lab_no_wiemels, 
+		:accession_no, :idno_wiemels, :studyid, :allow_nil => true
+
+	validates_format_of :email,
+	  :with => /\A([-a-z0-9!\#$%&'*+\/=?^_`{|}~]+\.)*[-a-z0-9!\#$%&'*+\/=?^_`{|}~]+@((?:[-a-z0-9]+\.)+[a-z]{2,})\Z/i, 
+		:allow_blank => true
+
+	validate :presence_of_guardian_relationship_other,
+		:if => :guardian_relationship_is_other?
+
+	validates_presence_of :birth_city,
+		:if => :birth_country_is_united_states?
+	validates_presence_of :birth_state,
+		:if => :birth_country_is_united_states?
+
+	validates_length_of :case_control_type, :is => 1, :allow_nil => true
+
+	validates_length_of     :ssn, :maximum => 250, :allow_nil => true
+	validates_uniqueness_of :ssn, :allow_nil => true
+	validates_format_of     :ssn, :with => /\A\d{3}-\d{2}-\d{4}\z/,
+		:message => "should be formatted ###-##-####", :allow_nil => true
+
+ 	validates_length_of :birth_year, 
+			:maximum => 4, :allow_blank => true
+	validates_length_of :newid, 
+			:maximum => 6, :allow_blank => true
+	validates_length_of :icf_master_id, 
+			:maximum => 9, :allow_blank => true
+	validates_length_of :childidwho, :idno_wiemels, 
+ 		:generational_suffix, :father_generational_suffix, 
+			:maximum => 10, :allow_blank => true
+	validates_length_of :lab_no_wiemels, :accession_no, 
+			:maximum => 25, :allow_blank => true
+	validates_length_of :gbid, 
+			:maximum => 26, :allow_blank => true
+	validates_length_of :first_name, :last_name, 
+		:middle_name, :maiden_name, :guardian_relationship_other,
+		:father_first_name, :father_middle_name, :father_last_name,
+		:mother_first_name, :mother_middle_name, :mother_maiden_name, :mother_last_name,
+		:guardian_first_name, :guardian_middle_name, :guardian_last_name,
+		:mother_race_other, :father_race_other,
+		:birth_city, :birth_state, :birth_country,
+		:state_id_no, :state_registrar_no, :local_registrar_no,
+		:lab_no, :related_childid, :related_case_childid,
+			:maximum => 250, :allow_blank => true
+
+
+	validates_inclusion_of :mom_is_biomom, :dad_is_biodad,
+			:in => YNDK.valid_values, :allow_nil => true
+
+
+	# custom validation for custom message without standard attribute prefix
+	def presence_of_sex
+		if sex.blank?
+			errors.add(:sex, ActiveRecord::Error.new(
+				self, :base, :blank, {
+					:message => "No sex has been chosen." } ) )
+		end
+	end
+
+protected
+
+	def birth_country_is_united_states?
+		birth_country == 'United States'
+	end
+
+	#	custom validation for custom message without standard attribute prefix
+	def presence_of_guardian_relationship_other
+		if guardian_relationship_other.blank?
+			errors.add(:guardian_relationship_other, ActiveRecord::Error.new(
+				self, :base, :blank, { 
+					:message => "You must specify a relationship with 'other relationship' is selected." } ) )
+		end
+	end
+
+	#	custom validation for custom message without standard attribute prefix
+	def presence_of_dob
+		if dob.blank?
+			errors.add(:dob, ActiveRecord::Error.new(
+				self, :base, :blank, { 
+					:message => "Date of birth can't be blank." } ) )
+		end
+	end
+
+end	#	class_eval
+end	#	included
+end	#	StudySubjectValidations
+
+__END__
+