ccls-ccls_engine 3.11.0

data/app/models/home_exposure_response.rb

@@ -0,0 +1,24 @@
+# Extraction of answers from the survey
+class HomeExposureResponse < ActiveRecordShared
+
+	belongs_to :study_subject
+	attr_protected :study_subject_id, :study_subject
+
+	#	NEEDS to be here to match the uniqueness index in the database.
+	validates_uniqueness_of :study_subject_id, :allow_nil => true
+
+	validates_length_of :additional_comments, :maximum => 65000, :allow_blank => true
+
+	def self.fields
+		#	db: db field name
+		#	human: humanized field
+		@@fields ||= YAML::load( ERB.new( IO.read(
+			File.join(File.dirname(__FILE__),'../../config/home_exposure_response_fields.yml')
+			)).result)
+	end
+
+	def self.db_field_names
+		fields.collect{|f|f[:db]}
+	end
+
+end

data/app/models/homex_outcome.rb

@@ -0,0 +1,75 @@
+# don't know exactly
+class HomexOutcome < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	belongs_to :study_subject
+	attr_protected :study_subject_id, :study_subject
+	belongs_to :sample_outcome
+	belongs_to :interview_outcome
+
+	validates_uniqueness_of :study_subject_id, :allow_nil => true
+	validates_presence_of   :sample_outcome_on,    :if => :sample_outcome_id?
+	validates_presence_of   :interview_outcome_on, :if => :interview_outcome_id?
+	validates_complete_date_for :interview_outcome_on, :allow_nil => true
+	validates_complete_date_for :sample_outcome_on,    :allow_nil => true
+
+	before_save :create_interview_outcome_update,
+		:if => :interview_outcome_id_changed?
+
+	before_save :create_sample_outcome_update,
+		:if => :sample_outcome_id_changed?
+
+	class NoHomeExposureEnrollment < StandardError	#	:nodoc:
+	end
+
+protected
+
+	#	Create OperationalEvent regarding the interview outcome
+	def create_interview_outcome_update
+		operational_event_type = case interview_outcome 
+			when InterviewOutcome['scheduled']
+				OperationalEventType['scheduled']
+			when InterviewOutcome['complete']
+				OperationalEventType['iv_complete']
+			else nil
+		end
+		unless operational_event_type.nil?
+			if hxe = study_subject.enrollments.find_by_project_id(Project['HomeExposures'].id)
+				OperationalEvent.create!(
+					:enrollment => hxe,
+					:operational_event_type => operational_event_type,
+					:occurred_on => interview_outcome_on
+				)
+			else
+				raise NoHomeExposureEnrollment 
+			end
+		end
+	end
+
+	#	Create OperationalEvent regarding the sample outcome
+	def create_sample_outcome_update
+		operational_event_type = case sample_outcome 
+			when SampleOutcome['sent']
+				OperationalEventType['kit_sent']
+			when SampleOutcome['received']
+				OperationalEventType['sample_received']
+			when SampleOutcome['complete']
+				OperationalEventType['sample_complete']
+			else nil
+		end
+		unless operational_event_type.nil?
+			if hxe = study_subject.enrollments.find_by_project_id(Project['HomeExposures'].id)
+				OperationalEvent.create!(
+					:enrollment => hxe,
+					:operational_event_type => operational_event_type,
+					:occurred_on => sample_outcome_on
+				)
+			else
+				raise NoHomeExposureEnrollment 
+			end
+		end
+	end
+
+end

data/app/models/hospital.rb

@@ -0,0 +1,22 @@
+class Hospital < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	belongs_to :organization
+
+	#	database will default to false
+	validates_inclusion_of :has_irb_waiver, :in => [ true, false ]
+
+	#	if organization_id is not unique, using find_by_organization_id as I do 
+	#	WILL cause problems as it will only ever return the first match
+	validates_presence_of   :organization_id
+	validates_presence_of   :organization, :if => :organization_id
+	validates_uniqueness_of :organization_id, :allow_blank => true
+
+	named_scope :waivered,    :conditions => { :has_irb_waiver => true }
+	named_scope :nonwaivered, :conditions => { :has_irb_waiver => false }
+
+	delegate :to_s, :to => :organization, :allow_nil => true
+
+end

data/app/models/icf_master_id.rb

@@ -0,0 +1,30 @@
+class IcfMasterId < ActiveRecordShared
+
+#+------------------+------------+------+-----+---------+----------------+
+#| Field            | Type       | Null | Key | Default | Extra          |
+#+------------------+------------+------+-----+---------+----------------+
+#| id               | int(11)    | NO   | PRI | NULL    | auto_increment |
+#| icf_master_id    | varchar(9) | YES  | UNI | NULL    |                |
+#| assigned_on      | date       | YES  |     | NULL    |                |
+#| created_at       | datetime   | YES  |     | NULL    |                |
+#| updated_at       | datetime   | YES  |     | NULL    |                |
+#| study_subject_id | int(11)    | YES  | UNI | NULL    |                |
+#+------------------+------------+------+-----+---------+----------------+
+
+	belongs_to :study_subject
+  attr_protected( :study_subject_id, :study_subject )
+
+#	probably shouldn't add validations as this won't be created by users. yet.
+
+	def to_s
+		icf_master_id
+	end
+
+#	a named scope would be nice but
+	def self.next_unused
+		find(:first,
+			:conditions => ['study_subject_id IS NULL']
+		)
+	end
+
+end

data/app/models/icf_master_tracker.rb

@@ -0,0 +1,217 @@
+class IcfMasterTracker < ActiveRecordShared
+
+#	can I attr_protected for update only?
+#	or perhaps find_or_create_by_masterid?
+#	Of course that may create the new_tracker_record
+#	And then on update it would create all the others?
+
+	validates_presence_of   :Masterid
+	validates_uniqueness_of :Masterid, :allow_blank => true
+	attr_protected :Masterid
+
+#	validate all string field lengths ?
+	validates_length_of :last_update_attempt_errors, :maximum => 65000, :allow_blank => true
+
+	belongs_to :study_subject
+	attr_protected( :study_subject_id, :study_subject )
+
+	before_save :attach_study_subject
+	before_save :flag_for_update
+	before_save :save_all_changes
+
+	named_scope :have_changed, :conditions => {
+		:flagged_for_update => true
+	}
+
+	#	This may not be the best way to update.
+	#	We may have to implement something like BackgrounDRb.
+	#	Updating the actual data may require a number of SQL searches
+	#	to find the appropriate columns which could consume enough
+	#	time to trigger a timeout. In addition, there may not be
+	#	enough information here to determine the correct model
+	#	to update, but we'll see how it progresses.
+	#	If we do use BackgrounDRb, we'll probably need an additional
+	#	column to flag has having been updated to be set in
+	#	a before_save callback.  This would then need unset by
+	#	the BackgrounDRb worker when complete.
+#	after_save  :update_models
+
+	def attach_study_subject
+		unless study_subject_id
+			self.study_subject = StudySubject.find_by_icf_master_id(self.Masterid)
+		end
+	end
+
+	def ignorable_changes
+#		%w{id flagged_for_update study_subject_id Masterid created_at updated_at}
+		%w{ id created_at updated_at
+			flagged_for_update last_update_attempt_errors last_update_attempted_at }
+	end
+
+	def unignorable_changes
+		changes.dup.delete_keys!(*ignorable_changes)
+	end
+
+	def flag_for_update
+		self.flagged_for_update = true unless unignorable_changes.empty?
+	end
+
+	def save_all_changes
+		if new_record?
+			IcfMasterTrackerChange.create(
+				:icf_master_id => self.Masterid,
+#  5       t.date :master_tracker_date	#	Hmm.
+				:new_tracker_record => true
+			)
+		else
+			unignorable_changes.each do |field,values|
+				IcfMasterTrackerChange.create(
+					:icf_master_id => self.Masterid,
+#  5       t.date :master_tracker_date	#	Hmm.
+					:modified_column => field,
+					:previous_value => values[0],
+					:new_value => values[1]
+				)
+			end
+		end
+	end
+
+	def self.update_models_flagged_for_update
+		puts "Searching for changed Icf Master Tracker records."
+		changed_records = self.have_changed
+		if changed_records.empty?
+			puts "- Found no changed records."
+		else
+			puts "- Found #{changed_records} changed records."
+			changed_records.each do |record|
+#				record.last_update_attempted_at = Time.now
+#				unless record.study_subject_id.nil?
+#					try to update models
+#					if successful
+#						record.flagged_for_update = false
+#						record.last_update_attempt_errors = nil
+#					else
+#						set last_update_attempt_error
+#						leave flagged_for_update as true
+#					end
+#				else
+#					record.last_update_attempt_errors = "study_subject is nil.  Nothing to update."
+#					leave flagged_for_update as true
+#				end
+#				record.save
+			end
+		end
+	end
+
+
+
+
+#		def update_models
+#	#
+#	#	"Masterid","Motherid","Record_Owner","Datereceived","Lastatt","Lastdisp",
+#	#	"Currphone","Vacauthrecd","Recollect","Needpreincentive","Active_Phone",
+#	#	"Recordsentformatching","Recordreceivedfrommatching","Sentpreincentive",
+#	#	"Releasedtocati","Confirmedcaticontact","Refused","Deceasednotification",
+#	#	"Eligible","Confirmationpacketsent","Catiprotocolexhausted",
+#	#	"Newphonenumreleasedtocati","Pleanotificationsent",
+#	#	"Casereturnedtoberkeleyfornewinf","Casereturnedfromberkeley","Caticomplete",
+#	#	"Kitmothersent","Kitinfantsent","Kitchildsent","Kitadolescentsent",
+#	#	"Kitmotherrefusedcode","Kitchildrefusedcode","Noresponsetoplea",
+#	#	"Responsereceivedfromplea","Senttoinpersonfollowup","Kitmotherrecd",
+#	#	"Kitchildrecvd","Thankyousent","Physrequestsent","Physresponsereceived"
+#	#
+#	#	Most of the columns are dates which probably correspond to an enrollment or sample.
+#	#Table: samples
+#	#+------------------------------+---------------
+#	#| Field                        | Type         
+#	#+------------------------------+--------------
+#	#| aliquot_sample_format_id     | int(11)      
+#	#| sample_type_id               | int(11)      
+#	#| study_subject_id             | int(11)      
+#	#| unit_id                      | int(11)      
+#	#| order_no                     | int(11)      
+#	#| quantity_in_sample           | decimal(10,0)
+#	#| aliquot_or_sample_on_receipt | varchar(255) 
+#	#| sent_to_subject_on           | date         
+#	#| received_by_ccls_on          | date        
+#	#| sent_to_lab_on               | date        
+#	#| received_by_lab_on           | date        
+#	#| aliquotted_on                | date        
+#	#| external_id                  | varchar(255)
+#	#| external_id_source           | varchar(255)
+#	#| receipt_confirmed_on         | date        
+#	#| receipt_confirmed_by         | varchar(255)
+#	#| future_use_prohibited        | tinyint(1)  
+#	#| collected_on                 | date       
+#	#| location_id                  | int(11)   
+#	#
+#	#		if study_subject_id and dirty
+#	#		Consider Record_Owner field?
+#	#		Which project?
+#	#			add operational event with differences to study subject
+#	#			update models
+#	#		end
+#	
+#			if study_subject_id and changed?
+#	#			puts
+#	#			puts "Tracker has subject and has changed so begin updating"
+#	#			puts self.changes
+#	#
+#	#			Which changes matter?
+#	#			There are many validations, so what to do if update fails?
+#	#			If subject doesn't initially exist (shouldn't happen),
+#	#				then these updates will NEVER be added as the record
+#	#				"changes" won't be changed.  Will need another condition
+#	#				to update everything if study_subject_id is new.
+#	#				Again, this shouldn't actually ever happen as the Masterid
+#	#				is assigned to a subject by us, meaning the subject exists
+#	#				before giving it to ICF.
+#	
+#	#			unignored_changes = changes.dup.delete_keys!(*ignorable_changes)
+#				unless unignorable_changes.empty?
+#	#				description = []
+#	#				unignorable_changes.each { |field,values|
+#	#					description << "#{field} changed from #{values[0]} to #{values[1]}"
+#	#				}
+#	#				OperationalEvent.create!(
+#	#					:enrollment => study_subject.enrollments.find_or_create_by_project_id(
+#	#						Project[:ccls].id),
+#	#					:operational_event_type => OperationalEventType[:other],
+#	##
+#	##	description can only be 250 chars so this fails in testing
+#	##		when creating new tracker as everything has changed.
+#	##	Change description to text?  Will 65000 chars be enough?
+#	##
+#	##					:description => description.join("\n")
+#	#					:description => "Icf Master Tracker caused changes."
+#	#				)
+#				end
+#	#		else
+#	#			puts
+#	#			puts "Tracker has no subject so skipping updating"
+#			end
+#		end
+
+end
+
+__END__
+
+
+changed?() public
+
+Returns true if any attribute have unsaved changes, false otherwise.
+
+person.changed? # => false
+person.name = 'bob'
+person.changed? # => true
+
+
+changes() public
+
+Map of changed attrs => [original value, new value].
+
+person.changes # => {}
+person.name = 'bob'
+person.changes # => { 'name' => ['bill', 'bob'] }
+
+

data/app/models/icf_master_tracker_change.rb

@@ -0,0 +1,9 @@
+class IcfMasterTrackerChange < ActiveRecordShared
+
+	#	Would be pointless without the icf_master_id
+	validates_presence_of :icf_master_id
+
+#	should probably avoid validations
+#	validates_inclusion_of :new_tracker_record, :in => [ true, false ]
+
+end

data/app/models/icf_master_tracker_update.rb

@@ -0,0 +1,50 @@
+class IcfMasterTrackerUpdate < ActiveRecordShared
+
+	has_attached_file :csv_file,
+		YAML::load(ERB.new(IO.read(File.expand_path(
+			File.join(File.dirname(__FILE__),'../..','config/icf_master_tracker_update.yml')
+		))).result)[Rails.env]
+
+
+	#	This doesn't really do much of anything yet.
+	def parse
+		results = []
+		if !self.csv_file_file_name.blank? &&
+				File.exists?(self.csv_file.path)
+			(f=FasterCSV.open( self.csv_file.path, 'rb',{
+				:headers => true })).each do |line|
+
+#	"Masterid","Motherid","Record_Owner","Datereceived","Lastatt","Lastdisp","Currphone","Vacauthrecd","Recollect","Needpreincentive","Active_Phone","Recordsentformatching","Recordreceivedfrommatching","Sentpreincentive","Releasedtocati","Confirmedcaticontact","Refused","Deceasednotification","Eligible","Confirmationpacketsent","Catiprotocolexhausted","Newphonenumreleasedtocati","Pleanotificationsent","Casereturnedtoberkeleyfornewinf","Casereturnedfromberkeley","Caticomplete","Kitmothersent","Kitinfantsent","Kitchildsent","Kitadolescentsent","Kitmotherrefusedcode","Kitchildrefusedcode","Noresponsetoplea","Responsereceivedfromplea","Senttoinpersonfollowup","Kitmotherrecd","Kitchildrecvd","Thankyousent","Physrequestsent","Physresponsereceived"
+
+#
+#	The IcfMasterTracker will include an after_save or something that will
+#	determine what has changed and update appropriately.  It may also
+#	create OperationalEvents to document the data changes.  As it is
+#	theoretically possible that the Masterid does not exist in the identifiers
+#	table, perhaps add a successfully_updated_models flag which could
+#	be used?
+#
+				icf_master_tracker = IcfMasterTracker.find_or_create_by_Masterid(line['Masterid'])
+				#	NO BANG. Don't want to raise any errors.
+				successfully_updated = icf_master_tracker.update_attributes(line.to_hash)
+#
+#	errors = icf_master_tracker.errors.full_messages.to_sentence
+#	These won't be validation errors as there shouldn't be any.
+#	Perhaps "no column by that name" errors if csv file changes?
+#
+#	Add successfully_updated value?
+#		icf_master_tracker.update_attribute(:sucessfully_updated, successfully_updated)
+#	will the above include the line's attributes?
+#
+#	Add update_errors column?
+#		icf_master_tracker.update_attribute(:update_errors, errors)
+#
+
+				results.push(icf_master_tracker)
+
+			end	#	(f=FasterCSV.open( self.csv_file.path, 'rb',{ :headers => true })).each
+		end	#	if !self.csv_file_file_name.blank? && File.exists?(self.csv_file.path)
+		results	#	TODO why am I returning anything?  will I use this later?
+	end	#	def parse
+
+end

data/app/models/ineligible_reason.rb

@@ -0,0 +1,26 @@
+#	==	requires
+#	*	description (unique and > 3 chars)
+class IneligibleReason < ActiveRecordShared
+
+	acts_as_list
+	default_scope :order => :position
+
+	acts_like_a_hash
+
+	has_many :enrollments
+
+	validates_length_of     :ineligible_context, 
+		:maximum => 250, :allow_blank => true
+
+	#	Returns description
+	def to_s
+		description
+	end
+
+	#	Returns boolean of comparison
+	#	true only if key == 'other'
+	def is_other?
+		key == 'other'
+	end
+
+end