Module: StudySubjectIdentifier

Included in:
StudySubject
Defined in:
app/models/study_subject_identifier.rb

Overview

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.

Class Method Summary collapse

Class Method Details

.included(base) ⇒ Object 



7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
 
# File 'app/models/study_subject_identifier.rb', line 7

def self.included(base)
#	Must delay the calls to these ActiveRecord methods
#	or it will raise many "undefined method"s.
base.class_eval do

	#	Very cool that this doesn't stop factory girl from using them.
	#	it will stop the study_subject nested_attribute tests though
	attr_protected :studyid, :studyid_nohyphen, :studyid_intonly_nohyphen,
		:familyid, :childid, :subjectid, :patid, :orderno

	before_validation :prepare_fields_for_validation
	before_create     :prepare_fields_for_creation

	def self.find_all_by_studyid_or_icf_master_id(studyid,icf_master_id)
#	if decide to use LIKE, will need to NOT include nils so
#	will need to add some conditions to the conditions.
		self.find( :all, 
			:conditions => [
				"studyid = :studyid OR icf_master_id = :icf_master_id",
				{ :studyid => studyid, :icf_master_id => icf_master_id }
			]
		)
	end

protected

	def prepare_fields_for_validation
		#	NOTE ANY field that has a unique index in the database NEEDS
		#	to NOT be blank.  Multiple nils are acceptable in index,
		#	but multiple blanks are NOT.  Nilify ALL fields with
		#	unique indexes in the database.
		self.email = nil if email.blank?
		self.ssn = nil if ssn.blank?
		self.state_id_no = nil if state_id_no.blank?
		self.state_registrar_no = nil if state_registrar_no.blank?
		self.local_registrar_no = nil if local_registrar_no.blank?
		self.gbid = nil if gbid.blank?
		self.lab_no_wiemels = nil if lab_no_wiemels.blank?
		self.accession_no = nil if accession_no.blank?
		self.idno_wiemels = nil if idno_wiemels.blank?

		self.case_control_type = ( ( case_control_type.blank? 
			) ? nil : case_control_type.to_s.upcase )

		patid.try(:gsub!,/\D/,'')
		self.patid = sprintf("%04d",patid.to_i) unless patid.blank?

		matchingid.try(:gsub!,/\D/,'')
#	TODO add more tests for this (try with valid? method)
#puts "Matchingid before before validation:#{matchingid}"
		self.matchingid = sprintf("%06d",matchingid.to_i) unless matchingid.blank?
	end

	#	made separate method so can be stubbed
	def get_next_childid
		self.class.maximum(:childid).to_i + 1
	end

	#	made separate method so can be stubbed
	def get_next_patid
		self.class.maximum(:patid).to_i + 1
#
#	What happens if/when this goes over 4 digits? 
#	The database field is only 4 chars.
#
	end

	#	fields made from fields that WON'T change go here
	def prepare_fields_for_creation
		#	don't assign if given or is mother (childid is currently protected)
		self.childid = get_next_childid if !is_mother? and childid.blank?

		#	don't assign if given or is not case (patid is currently protected)
		self.patid = sprintf("%04d",get_next_patid.to_i) if is_case? and patid.blank?

#	should move this from pre validation to here for ALL subjects.
#		patid.try(:gsub!,/\D/,'')
#		self.patid = sprintf("%04d",patid.to_i) unless patid.blank?

		#	don't assign if given or is not case (orderno is currently protected)
		self.orderno = 0 if is_case? and orderno.blank?

		#	don't assign if given or is mother (studyid is currently protected)
		#	or if can't make complete studyid
		if !is_mother? and studyid.blank? and
				!patid.blank? and !case_control_type.blank? and !orderno.blank?
			self.studyid = "#{patid}-#{case_control_type}-#{orderno}" 
		end

		#	perhaps put in an after_save with an update_attribute(s)
		#	and simply generate a new one until all is well
		#	don't assign if given (subjectid is currently protected)
		self.subjectid = generate_subjectid if subjectid.blank?

		#	cases and controls: their own subjectID is also their familyID.
		#	mothers: their child's subjectID is their familyID. That is, 
		#					a mother and her child have identical familyIDs.
		#	don't assign if given (familyid is currently protected)
		self.familyid  = subjectid if !is_mother? and familyid.blank?

		#	cases (patients): matchingID is the study_subject's own subjectID
		#	controls: matchingID is subjectID of the associated case 
		#		(like PatID in this respect).
		#	mothers: matchingID is subjectID of their own child's associated case. 
		#			That is, a mother's matchingID is the same as their child's. This 
		#			will become clearer when I provide specs for mother study_subject creation.
#	matchingid is manually set in some tests.  will need to setup for stubbing this.
		#	don't assign if given (matchingid is currently NOT protected)
		self.matchingid = subjectid if is_case? and matchingid.blank?
	end

	#	made separate method so can stub it in testing
	#	This only guarantees uniqueness before creation,
	#		but not at creation. This is NOT scalable.
	#	Fortunately, we won't be creating tons of study_subjects
	#		at the same time so this should not be an issue,
	#		however, when it fails, it will be confusing.	#	TODO
	#	How to rescue from ActiveRecord::RecordInvalid here?
	#		or would it be RecordNotSaved?
#
#	Perhaps treat subjectid like icf_master_id?
#	Create a table with all of the possible 
#		subjectid ... (1..999999)
#		study_subject_id
#		assigned_on
#	Then select a random unassigned one?
#	Would this be faster?
#
	def generate_subjectid
		subjectids = ( (1..999999).to_a - self.class.find(:all,:select => 'subjectid'
			).collect(&:subjectid).collect(&:to_i) )
		#	CANNOT have leading 0' as it thinks its octal and converts
		#>> sprintf("%06d","0001234")
		#=> "000668"
		#
		# CANNOT have leading 0's and include and 8 or 9 as it thinks its octal
		# so convert back to Integer first
		#>> sprintf("%06d","0001280")
		#ArgumentError: invalid value for Integer: "0001280"
		# from (irb):24:in `sprintf'
		# from (irb):24
		sprintf("%06d",subjectids[rand(subjectids.length)].to_i)
	end

end	#	class_eval
end