ccls-ccls_engine 3.11.0

data/app/models/operational_event_type.rb

@@ -0,0 +1,31 @@
+#	==	requires
+#	*	key ( unique )
+#	*	description ( unique and > 3 chars )
+class OperationalEventType < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :operational_events
+
+	validates_presence_of   :event_category
+	validates_uniqueness_of :event_category
+	validates_length_of     :event_category, 
+		:in => 4..250, :allow_blank => true
+
+	#	Returns event_category.
+	def to_s
+		"#{event_category}:#{description}"
+	end
+
+	def self.categories
+		find(:all,
+			:conditions => 'event_category IS NOT NULL',
+			:order => 'event_category ASC',
+			:group => :event_category
+		).collect(&:event_category)
+	end
+
+end

data/app/models/organization.rb

@@ -0,0 +1,28 @@
+#	==	requires
+#	*	name ( unique and > 3 chars )
+class Organization < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash(:value => :name)
+
+	belongs_to :person
+	has_many :aliquots, :foreign_key => 'owner_id'
+	has_many :incoming_transfers, :class_name => 'Transfer', 
+		:foreign_key => 'to_organization_id'
+	has_many :outgoing_transfers, :class_name => 'Transfer', 
+		:foreign_key => 'from_organization_id'
+#	has_many :hospitals
+	has_one  :hospital
+	has_many :patients
+
+	validates_presence_of   :name
+	validates_uniqueness_of :name
+
+	#	Returns name
+	def to_s
+		name
+	end
+
+end

data/app/models/patient.rb

@@ -0,0 +1,63 @@
+# Patient related study_subject info.
+class Patient < ActiveRecordShared
+
+	belongs_to :study_subject
+	belongs_to :organization
+	belongs_to :diagnosis
+
+	delegate :is_other?, :to => :diagnosis, :allow_nil => true, :prefix => true
+
+	attr_protected( :study_subject_id, :study_subject )
+
+	include PatientValidations
+
+	#	Would it be better to do this before_validation?
+	before_save :format_raf_zip, :if => :raf_zip_changed?
+
+	after_save :trigger_update_matching_study_subjects_reference_date,
+		:if => :admit_date_changed?
+
+	after_save :trigger_setting_was_under_15_at_dx,
+		:if => :admit_date_changed?
+
+protected
+
+	#	Simply squish the zip removing leading and trailing spaces.
+	def format_raf_zip
+		#	zip was nil during import and skipping validations
+		self.raf_zip.squish! unless raf_zip.nil?
+		# convert to 12345-1234
+		if !self.raf_zip.nil? and self.raf_zip.length > 5
+			old = self.raf_zip.gsub(/\D/,'')
+			self.raf_zip = "#{old[0..4]}-#{old[5..8]}"
+		end
+	end
+
+	def trigger_setting_was_under_15_at_dx
+		logger.debug "DEBUG: calling update_patient_was_under_15_at_dx from Patient:#{self.attributes['id']}"
+		logger.debug "DEBUG: Admit date changed from:#{admit_date_was}:to:#{admit_date}"
+		if study_subject
+			logger.debug "DEBUG: study_subject:#{study_subject.id}"
+			study_subject.update_patient_was_under_15_at_dx
+		else
+			#	This should never happen, except in testing.
+			logger.warn "WARNING: Patient(#{self.attributes['id']}) is missing study_subject"
+		end
+	end
+#
+#	logger levels are ... debug, info, warn, error, and fatal.
+#
+	def trigger_update_matching_study_subjects_reference_date
+		logger.debug "DEBUG: calling update_study_subjects_reference_date_matching from Patient:#{self.attributes['id']}"
+		logger.debug "DEBUG: Admit date changed from:#{admit_date_was}:to:#{admit_date}"
+		if study_subject
+			logger.debug "DEBUG: study_subject:#{study_subject.id}"
+			# study_subject.update_matching_study_subjects_reference_date
+			study_subject.update_study_subjects_reference_date_matching
+		else
+			#	This should never happen, except in testing.
+			logger.warn "WARNING: Patient(#{self.attributes['id']}) is missing study_subject"
+		end
+	end
+
+end

data/app/models/patient_validations.rb

@@ -0,0 +1,118 @@
+#
+#	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 PatientValidations
+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 :admit_date
+	validate :presence_of_organization_id
+	validates_presence_of :diagnosis_id
+	validate :presence_of_hospital_no
+	validates_length_of   :hospital_no, :maximum => 25, :allow_blank => true
+	validates_uniqueness_of :hospital_no, :scope => :organization_id
+	validates_past_date_for :admit_date
+	validates_past_date_for :diagnosis_date
+	validates_past_date_for :treatment_began_on
+	validate :admit_date_is_after_dob
+	validate :diagnosis_date_is_after_dob
+	validate :treatment_began_on_is_after_diagnosis_date
+	validate :subject_is_case
+	validates_complete_date_for :admit_date,         :allow_nil => true
+	validates_complete_date_for :diagnosis_date,     :allow_nil => true
+	validates_complete_date_for :treatment_began_on, :allow_nil => true
+
+	validates_length_of :raf_zip, :maximum => 10, :allow_blank => true
+
+	validates_format_of :raf_zip,
+		:with => /\A\s*\d{5}(-)?(\d{4})?\s*\z/,
+		:message => "should be 12345 or 12345-1234",
+		:allow_blank => true
+
+	validates_presence_of :other_diagnosis, :if => :diagnosis_is_other?
+
+
+	validates_inclusion_of :was_under_15_at_dx, :was_previously_treated,
+		:was_ca_resident_at_diagnosis,
+			:in => YNDK.valid_values, :allow_nil => true
+
+
+protected
+
+	##
+	#	This validation does not work when using nested attributes as 
+	#	the study_subject has not been resolved yet, unless this is an update.
+	#	This results in a similar validation in Subject.
+	def admit_date_is_after_dob
+		if !admit_date.blank? && 
+			!study_subject.blank? && 
+			!study_subject.dob.blank? && 
+			study_subject.dob.to_date != Date.parse('1/1/1900') &&
+			admit_date < study_subject.dob &&
+			admit_date.to_date != Date.parse('1/1/1900')
+			errors.add(:admit_date, "is before study_subject's dob.") 
+		end
+	end
+
+	##
+	#	This validation does not work when using nested attributes as 
+	#	the study_subject has not been resolved yet, unless this is an update.
+	#	This results in a similar validation in Subject.
+	def diagnosis_date_is_after_dob
+		if !diagnosis_date.blank? && 
+			!study_subject.blank? && 
+			!study_subject.dob.blank? && 
+			diagnosis_date < study_subject.dob
+			errors.add(:diagnosis_date, "is before study_subject's dob.") 
+		end
+	end
+
+	##
+	#	Both are patient dates so this doesn't need in subject!
+	#	custom validation and custom message
+	def treatment_began_on_is_after_diagnosis_date
+		if !treatment_began_on.blank? && 
+			!diagnosis_date.blank? && 
+			treatment_began_on < diagnosis_date
+#			errors.add(:treatment_began_on, "is before diagnosis_date.") 
+			errors.add(:treatment_began_on, ActiveRecord::Error.new(
+				self, :base, :blank, { 
+					:message => "Date treatment began must be on or after the diagnosis date." } ) )
+		end
+	end
+
+	##
+	#	This validation does not work when using nested attributes as 
+	#	the study_subject has not been resolved yet, unless this is an update.
+	#	This results in a similar validation in Subject.
+	def subject_is_case
+		if study_subject and !study_subject.is_case?
+			errors.add(:study_subject,"must be case to have patient info")
+		end
+	end
+
+	#	custom validation for custom message without standard attribute prefix
+	def presence_of_organization_id
+		if organization_id.blank?
+			errors.add(:organization_id, ActiveRecord::Error.new(
+				self, :base, :blank, { 
+					:message => "Treating institution can't be blank." } ) )
+		end
+	end
+
+	#	custom validation for custom message without standard attribute prefix
+	def presence_of_hospital_no
+		if hospital_no.blank?
+			errors.add(:hospital_no, ActiveRecord::Error.new(
+				self, :base, :blank, { 
+					:message => "Hospital record number can't be blank." } ) )
+		end
+	end
+
+end	#	class_eval
+end	#	included
+end	#	PatientValidations

data/app/models/person.rb

@@ -0,0 +1,28 @@
+# don't know exactly
+class Person < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+#	belongs_to :context
+	has_many :interviews, :foreign_key => 'interviewer_id'
+	has_many :organizations
+
+	validates_presence_of :last_name
+	validates_length_of   :first_name, :maximum => 250, :allow_blank => true
+	validates_length_of   :last_name,  :maximum => 250, :allow_blank => true
+	validates_length_of   :honorific,  :maximum => 250, :allow_blank => true
+
+	named_scope :interviewers, :conditions => { :person_type_id => 3 }
+
+	#	Returns string containing first and last name
+	def full_name
+		"#{first_name} #{last_name}"
+	end
+
+	#	Returns full_name
+	def to_s
+		full_name
+	end
+
+end

data/app/models/phone_number.rb

@@ -0,0 +1,105 @@
+# A study_subject's phone number
+class PhoneNumber < ActiveRecordShared
+
+	acts_as_list :scope => :study_subject_id
+	default_scope :order => :position
+
+	belongs_to :study_subject
+	belongs_to :phone_type
+	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
+
+	validates_presence_of :phone_number
+
+	validates_presence_of :phone_type_id
+	validates_presence_of :phone_type, :if => :phone_type_id
+
+	validates_presence_of :why_invalid,       :if => :is_not_valid?
+	validates_presence_of :how_verified,      :if => :is_verified?
+	validates_presence_of :data_source_other, :if => :data_source_is_other?
+	validates_length_of   :why_invalid,  :maximum => 250, :allow_blank => true
+	validates_length_of   :how_verified, :maximum => 250, :allow_blank => true
+
+	#	Want to ensure contains 10 digits.
+	#	I'm kinda surprised that this regex works.
+	validates_format_of   :phone_number, :with => /\A(\D*\d\D*){10}\z/,
+		:allow_blank => true
+
+
+
+
+	attr_protected :study_subject_id, :study_subject
+
+
+
+
+	validates_inclusion_of :current_phone, :is_valid,
+			:in => YNDK.valid_values, :allow_nil => true
+
+
+	named_scope :current, :conditions => [
+		'current_phone IS NOT NULL AND current_phone != 2'
+	]
+
+	named_scope :historic, :conditions => [
+		'current_phone IS NULL OR current_phone = 2'
+	]
+
+	before_save :format_phone_number, :if => :phone_number_changed?
+
+	before_save :set_verifier, 
+		:if => :is_verified?, 
+		:unless => :is_verified_was
+
+	before_save :nullify_verifier, 
+		:unless => :is_verified?,
+		:if => :is_verified_was
+
+	attr_accessor :current_user
+
+	#	Returns description
+	def to_s
+		phone_number
+	end
+
+	#	Returns boolean of comparison
+	#	true only if is_valid == 2 or 999
+	#	Beware of strings from forms
+	#	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
+
+	#	Formats phone numer with () and -
+	def format_phone_number
+		unless self.phone_number.nil?
+			old = self.phone_number.gsub(/\D/,'')
+			new_phone = "(#{old[0..2]}) #{old[3..5]}-#{old[6..9]}"
+			self.phone_number = new_phone
+		end
+	end
+
+end

data/app/models/phone_type.rb

@@ -0,0 +1,15 @@
+# The type of phone number (home,work,mobile,etc.)
+class PhoneType < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+	has_many :phone_numbers
+
+	#	Returns key
+	def to_s
+		key
+	end
+
+end

data/app/models/project.rb

@@ -0,0 +1,39 @@
+#	==	requires
+#	*	key ( unique )
+#	*	description ( unique and > 3 chars )
+class Project < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+#	has_many :operational_event_types
+	has_many :instrument_types
+	has_many :enrollments
+	has_many :samples
+	has_many :gift_cards
+	has_many :study_subjects, :through => :enrollments
+	has_many :instruments
+
+	validates_complete_date_for :began_on, :allow_nil => true
+	validates_complete_date_for :ended_on, :allow_nil => true
+	validates_length_of :eligibility_criteria, :maximum => 65000, :allow_blank => true
+
+#	TODO perhaps move this into study_subject where is clearly belongs, but will need a RIGHT JOIN or something?
+	#	Returns all projects for which the study_subject
+	#	does not have an enrollment
+	def self.unenrolled_projects(study_subject)
+		Project.all(
+			:joins => "LEFT JOIN enrollments ON " <<
+				"projects.id = enrollments.project_id AND " <<
+				"enrollments.study_subject_id = #{study_subject.id}",
+			:conditions => [ "enrollments.study_subject_id IS NULL" ])
+	end
+
+	#	Returns description
+	def to_s
+		description
+	end
+
+end

data/app/models/project_outcome.rb

@@ -0,0 +1,19 @@
+class ProjectOutcome < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :enrollments
+
+#	validates_presence_of   :code
+#	validates_uniqueness_of :code
+#	validates_length_of     :code, :maximum => 250, :allow_blank => true
+
+	#	Returns description
+	def to_s
+		description
+	end
+
+end