caruby-tissue 1.4.2 → 1.5.1

data/lib/catissue/domain/transfer_event_parameters.rb

@@ -31,7 +31,7 @@ module CaTissue
       location
     end
 
-    add_attribute(:from)
+    add_attribute(:from, Location)
 
     # Returns the to Location.
     def to
@@ -46,6 +46,6 @@ module CaTissue
       self.to_column = location.column
     end
 
-    add_attribute(:to)
+    add_attribute(:to, Location)
   end
 end

data/lib/catissue/domain/user.rb

@@ -10,9 +10,9 @@ module CaTissue
   class User
     include Person
 
-    # caTissue alert - work-around for caTissue Bug #66 - Client missing CSException class et al.
-    # caTissue User class initializes roleId to "", which triggers a client exception on subsequent
-    # getRoleId call. Use a private variable instead and bypass getRoleId.
+    # @quirk caTissue work-around for caTissue Bug #66 - Client missing CSException class et al.
+    #   caTissue User class initializes roleId to "", which triggers a client exception on subsequent
+    #   getRoleId call. Use a private variable instead and bypass getRoleId.
     def role_id
       # TODO - uncomment following and get rid of @role_id i.v. when bug is fixed.
       #value = send(old_method)
@@ -24,8 +24,8 @@ module CaTissue
     # Sets the role id to the given value, which can be either a String or an Integer.
     # An empty or zero value is converted to nil.
     #
-    # caTissue alert - caTissue API roleId is a String although the intended value domain is the
-    # integer csm_role.identifier.
+    # @quirk caTissue caTissue API roleId is a String although the intended value domain is the
+    #   integer csm_role.identifier.
     def role_id=(value)
       # value as an integer (nil is zero)
       value_i = value.to_i
@@ -37,14 +37,14 @@ module CaTissue
       setRoleId(value_s)
     end
 
-    # caTissue alert - caTissue 1.2 User has an adminuser Java property, but caTissue throws an
-    # UnsupportedOperationException if they are called.
+    # @quirk caTissue caTissue 1.2 User has an adminuser Java property, but caTissue throws an
+    #   UnsupportedOperationException if they are called.
     if attribute_defined?(:adminuser) then remove_attribute(:adminuser) end
 
-    # make the convenience Person name a first-class attribute
-    add_attribute(:name)
+    # make the convenience {, CaRuby::Person::Name} name a first-class attribute
+    add_attribute(:name, CaRuby::Person::Name)
 
-    # caTissue alert - clinical study is unsupported by 1.1.x caTissue, removed in 1.2.
+    # @quirk caTissue clinical study is unsupported by 1.1.x caTissue, removed in 1.2.
     if attribute_defined?(:clinical_studies) then remove_attribute(:clinical_studies) end
 
     # clarify that collection_protocols is a coordinator -> protocol association.
@@ -63,16 +63,16 @@ module CaTissue
     # * initial password is 'changeMe1'
     add_attribute_defaults(:activity_status => 'Active', :page_of => 'pageOfUserAdmin', :role_id => 7, :new_password => 'changeMe1')
 
-    # caTissue alert - obscure GUI artifact User page_of attribute pollutes the data layer as a
-    # required attribute. Work-around is to simulate the GUI with a default value.
+    # @quirk caTissue obscure GUI artifact User page_of attribute pollutes the data layer as a
+    #   required attribute. Work-around is to simulate the GUI with a default value.
     add_mandatory_attributes(:activity_status, :address, :cancer_research_group, :department,
       :email_address, :first_name, :institution, :last_name, :page_of, :role_id)
 
-    # caTissue alert - User address can be created but not updated in 1.2.
+    # @quirk caTissue User address can be created but not updated in 1.2.
     #
-    # caTissue alert - User address is not fetched on create in 1.2.
+    # @quirk caTissue User address is not fetched on create in 1.2.
     #
-    # caRuby alert - adding the :saved_fetch qualifier results in JRuby load_error. TODO - fix this.
+    # @quirk caRuby adding the :saved_fetch qualifier results in JRuby load_error. TODO - fix this.
     add_dependent_attribute(:address)
 
     # Password cannot be saved in 1.2.

data/lib/catissue/extract/extractor.rb

@@ -46,7 +46,7 @@ module CaTissue
         fld = mapper.header(path)
         # the path node is either an attribute symbol or attribute metadata;
         # if metadata, then use the reader method.
-        @fld_path_hash[fld] = path.map { |attr_or_md| CaRuby::AttributeMetadata === attr_or_md ? attr_or_md.reader : attr_or_md }
+        @fld_path_hash[fld] = path.map { |attr_or_md| CaRuby::Domain::Attribute === attr_or_md ? attr_or_md.reader : attr_or_md }
       end
       logger.debug { "Extract field => path map: #{@fld_path_hash.transform { |path| path.join('.') }.pp_s}" }
     end

data/lib/catissue/resource.rb

@@ -1,14 +1,7 @@
 require 'caruby/resource'
-require 'caruby/domain/resource_module'
 require 'catissue/annotation/annotatable'
-require 'catissue/wustl/logger'
 
 module CaTissue
-  extend CaRuby::ResourceModule
-  
-  # Set up the caTissue client logger.
-  Wustl::Logger.configure
-
   # The module included by all CaTissue domain classes.
   #
   # A Resource class is extended to support an attribute -> value hash argument
@@ -40,14 +33,14 @@ module CaTissue
     # Returns the required attributes which are nil for this domain object.
     # Overrides the CaRuby::Resource method to handle the following bug:
     #
-    # caTissue alert - Bug #67:  AbstractSpecimen.setActivityStatus
-    # is a no-op. The Specimen activityStatus property is incorrectly pulled
-    # up to AbstractSpecimen. AbstractSpecimen.activityStatus is marked as
-    # mandatory, since it is required for Specimen. However, it is not
-    # mandatory, and in fact can't be set, for SpecimenRequirement.
-    # Work-around is to add special code to exclude activityStatus from
-    # the caRuby SpecimenRequirement missing mandatory attributes validation
-    # check.
+    # @quirk caTissue Bug #67:  AbstractSpecimen.setActivityStatus
+    #   is a no-op. The Specimen activityStatus property is incorrectly pulled
+    #   up to AbstractSpecimen. AbstractSpecimen.activityStatus is marked as
+    #   mandatory, since it is required for Specimen. However, it is not
+    #   mandatory, and in fact can't be set, for SpecimenRequirement.
+    #   Work-around is to add special code to exclude activityStatus from
+    #   the caRuby SpecimenRequirement missing mandatory attributes validation
+    #   check.
     def missing_mandatory_attributes
       invalid = super
       # Special case: AbstractSpecimen.setActivityStatus is a no-op.
@@ -72,26 +65,5 @@ module CaTissue
       value.nil? or value == UNSPECIFIED
     end
   end
-
-  # The include mix-in module.
-  @mixin = Resource
-
-  # The required Java package name.
-  @java_package = 'edu.wustl.catissuecore.domain'
-
-  # Extends the given domain class as an #{AnnotatableClass}.
-  #
-  # @param [Class] klass the class that was added to this domain module
-  def self.class_added(klass)
-    # Defer loading AnnotatableClass to avoid pulling in Database, which in turn
-    # attempts to import java classes before the path is established. Obscure
-    # detail, but don't know how to avoid it.
-    require 'catissue/annotation/annotatable_class'
-    klass.extend(AnnotatableClass)
-  end
-
-  # Load the domain class definitions.
-  dir = File.join(File.dirname(__FILE__), 'domain')
-  load_dir(dir)
 end
 

data/lib/catissue/util/location.rb

@@ -7,8 +7,6 @@ module CaTissue
   # Location does not capture the occupant; therefore, changing a location coordinate value alone does not
   # change the storage assignment of an occupant.
   class Location
-    include Comparable
-
     attr_accessor :container, :coordinate
 
     alias_attribute(:holder, :container)
@@ -55,17 +53,6 @@ module CaTissue
       super rescue false
     end
 
-    # @param [Location] other the position to compare
-    # @return (see Coordinate#<=>)
-    # @raise [ArgumentError] if other is not an Location
-    def <=>(other)
-      raise ArgumentError.new("Can't compare #{qp} to #{other.qp}") unless @container and Location === other
-      unless container == other.container then
-        raise ArgumentError.new("Can't compare #{qp} in container #{container} to #{other.qp} in container #{other.container}")
-      end
-      @coordinate <=> other.coordinate
-    end
-
     # @return [Location, nil] a new Location at the next slot in this Location's {#container},
     #   or nil if there are no more locations
     def succ

data/lib/catissue/util/person.rb

@@ -15,6 +15,8 @@ module CaTissue
 
     # Sets this Person's name to the name string or Name object.
     # A string name argument is parsed using Name.parse.
+    #
+    # @quirk caTissue CaTissue person names are inconsistent: Participant has a middle name, User doesn't.
     def name=(value)
       value = Name.parse(value) if String === value
       # a missing name is equivalent to an empty name for our purposes here
@@ -24,7 +26,6 @@ module CaTissue
       end
       self.first_name = value.first
       self.last_name = value.last
-      # caTissue alert - CaTissue person names are inconsistent: Participant has a middle name, User doesn't.
       self.middle_name = value.middle if respond_to?(:middle_name)
     end
   end

data/lib/catissue/util/position.rb

@@ -7,16 +7,6 @@ module CaTissue
   # and holder methods. The occupant must be a {Storable}. The holder must be
   # a {Container}.
   module Position
-    include Comparable
-
-    # @param [Position] other the position to compare
-    # @return (see Location#<=>)
-    # @raise [ArgumentError] if other is not an instance of this Position's concrete class
-    def <=>(other)
-      raise ArgumentError.new("Can't compare #{qp} to #{other.qp}") unless self.class === other
-      equal?(other) ? 0 : location <=> other.location
-    end
-
     # @return [Boolean] whether other is an instance of this position's class with the same
     #   occupant and equal location
     #
@@ -30,7 +20,7 @@ module CaTissue
       location.coordinate
     end
     
-    # @return [Location] the location of this Position.
+    # @return [Location] the location of this Position
     def location
       @location ||= Location.new
       # always ensure that the location is consistent with the Java state

data/lib/catissue/util/uniquify.rb

@@ -7,7 +7,7 @@ module CaTissue
     # Makes this CP's short and long title unique.
     def uniquify
       super
-      self.title = short_title
+      self.short_title = title
     end
   end
 

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "1.4.2"
+  VERSION = "1.5.1"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2-1.2"

data/lib/catissue/wustl/logger.rb

@@ -2,23 +2,23 @@
 module Wustl
   # Logger configures the +edu.wustl+ logger.
   module Logger
-    # caTissue alert - the caTissue logger must be initialized before caTissue objects are created.
-    # The logger at issue is the caTissue client logger, not the caTissue server logger nor
-    # the caRuby logger. The caTissue logger facade class is edu.wustl.common.util.logger.Logger.
-    # In caTissue 1.1.x, initialization is done with +configure+, in 1.2 with
-    # +LoggerConfig.configureLogger+.
+    # @quirk caTissue the caTissue logger must be initialized before caTissue objects are created.
+    #   The logger at issue is the caTissue client logger, not the caTissue server logger nor
+    #   the caRuby logger. The caTissue logger facade class is edu.wustl.common.util.logger.Logger.
+    #   In caTissue 1.1.x, initialization is done with +configure+, in 1.2 with
+    #   +LoggerConfig.configureLogger+.
     #
-    # catTissue alert - +LoggerConfig.configureLogger+ expects file +log4j.properties+ in the class
-    # path. However, in 1.2 the client property file is +client_log4j.properties+. Work-around is
-    # as follows:
-    # * copy this file into the caRuby Tissue distribution as +conf/wustl/log4.properties+
-    # * add +conf/wustl+ to the classpath.
-    # * call +LoggerConfig.configureLogger+ with the config directory as an argument
+    # @quirk catTissue +LoggerConfig.configureLogger+ expects file +log4j.properties+ in the class
+    #   path. However, in 1.2 the client property file is +client_log4j.properties+. Work-around is
+    #   as follows:
+    #   * copy this file into the caRuby Tissue distribution as +conf/wustl/log4.properties+
+    #   * add +conf/wustl+ to the classpath.
+    #   * call +LoggerConfig.configureLogger+ with the config directory as an argument
     #
-    # caTissue alert - The caTissue client log location is unfortunately hard-coded in a caTissue client
-    # configuration file, does not create the parent directory on demand, and issues an obscure error
-    # message if the directory does not exist in release 1.1.x. The work-around is to ensure that the
-    # working directory contains a log subdirectory.
+    # @quirk caTissue The caTissue client log location is unfortunately hard-coded in a caTissue client
+    #   configuration file, does not create the parent directory on demand, and issues an obscure error
+    #   message if the directory does not exist in release 1.1.x. The work-around is to ensure that the
+    #   working directory contains a log subdirectory.
     def self.configure
       # Set the configured flag. Configure only once.
       if @configured then return else @configured = true end
@@ -40,8 +40,9 @@ module Wustl
 
     # Makes a +./log+ subdirectory to avoid a caTissue log initializer error. This method should be called
     # before configuring the logger.
+    #
+    # @quirk caTissue avoid caTissue error by creating log subdirectory.
     def self.ensure_log_directory_exists
-      # caTissue alert - avoid caTissue error by creating log subdirectory
       if File.directory?('log') then
         unless File.writable?('log') then
           raise StandardError.new("caTissue log subdirectory #{File.expand_path('log')} is not writable")

data/test/fixtures/lib/catissue/defaults_test_fixture.rb

@@ -55,15 +55,17 @@ module CaTissueTest
       domain_objects.each { |obj| obj.find(:create) unless obj.identifier or obj.class.dependent? }
     end
 
-    # Repopulates the defaults and makes a unique collection_protocol short_title, participant MRN and
-    # specimen label.
+    # Repopulates the defaults and makes the following attributes unique:
+    # * collection_protocol short title
+    # * participant MRN
+    # * specimen label
     #
     # @return this fixture
     def uniquify
       populate
       # make the CP and MRN unique; these values will ripple through the SCG, CPR, et al.
       # to make them unique as well
-      @protocol.short_title = @protocol.short_title.uniquify
+      @protocol.title = @protocol.title.uniquify
       @registration.participant.medical_identifiers.each { |mid| mid.medical_record_number = Uniquifier.qualifier }
       # unset the SCG name and specimen label so the default is set to a new unique value
       @specimen_collection_group.name = @specimen.label = nil
@@ -152,7 +154,7 @@ module CaTissueTest
 
       # the test collection protocol
       @protocol = CaTissue::CollectionProtocol.new(
-        :short_title => 'Test CP',
+        :title => 'Test CP',
         :principal_investigator => pi
       )
 

data/test/lib/catissue/domain/collection_protocol_test.rb

@@ -50,7 +50,6 @@ class CollectionProtocolTest < Test::Unit::TestCase
     assert(@pcl.specimens(pnt).include?(spc2), 'Specimen not found')
   end
 
-  # Verify the events.
   def test_events
     event = @pcl.events.first
     assert_not_nil(event, "Protocol test default has no events")

data/test/lib/catissue/domain/participant_test.rb

@@ -30,19 +30,70 @@ class ParticipantTest < Test::Unit::TestCase
     expected = @pnt.social_security_number = '555-55-5555'
     assert_equal(expected, @pnt.key, 'Person key is not the SSN')
   end
+
+  def test_treatment_annotation
+    trt = CaTissue::Participant::Clinical::TreatmentAnnotation.new
+    trt.merge_attributes(:agent => 'ACACIA', :participant => @pnt)
+    dur = CaTissue::Participant::Clinical::Duration.new
+    dur.merge_attributes(:start_date => DateTime.new(2010, 10, 10), :end_date => DateTime.new(2010, 12, 10), :treatment => trt)
+    cln = @pnt.clinical.first
+    assert_not_nil(cln, "Clinical annotation not added to participant")
+    trts = cln.treatment_annotations
+    assert_not_nil(trts.first, "Treatment not added to participant annotations")
+    assert_same(trt, trts.first, "Treatment incorrect")
+    assert_same(@pnt, trt.hook, "Treatment proxy hook not set")
+    assert_not_nil(trt.durations.first, "Duration not added to treatment annotation")
+    assert_same(dur, trt.durations.first, "Treatment duration incorrect")
+  end
+
+  def test_exposure_annotation
+    exp = CaTissue::Participant::Clinical::EnvironmentalExposuresHealthAnnotation.new
+    exp.merge_attributes(:years_agent_free => 2, :participant => @pnt)
+    cln = @pnt.clinical.first
+    assert_not_nil(cln, "Clinical annotation not added to participant")
+    exps = cln.environmental_exposures_health_annotations
+    assert_not_nil(exps.first, "Exposures not added to participant annotations")
+    assert_same(exp, exps.first, "Exposures incorrect")
+    assert_same(@pnt, exp.hook, "Exposure proxy hook not set")
+  end
+  
+  def test_alcohol_annotation
+    alc = CaTissue::Participant::Clinical::AlcoholHealthAnnotation.new
+    alc.merge_attributes(:drinks_per_week => 4, :years_agent_free => 2, :participant => @pnt)
+    cln = @pnt.clinical.first
+    assert_not_nil(cln, "Clinical annotation not added to participant")
+    alcs = cln.alcohol_health_annotations
+    assert_not_nil(alcs.first, "Alcohol health not added to participant annotations")
+    assert_same(alc, alcs.first, "Alcohol health incorrect")
+    assert_same(@pnt, alc.hook, "Alcohol health proxy hook not set")
+  end
   
   # Tests making a participant lab annotation. 
   def test_lab_annotation
-    labs = @pnt.lab_annotations
-    assert(labs.empty?, "Labs not empty at start")
     lab = CaTissue::Participant::Clinical::LabAnnotation.new
     lab.merge_attributes(:lab_test_name => 'Test Lab', :participant => @pnt)
-    labs = @pnt.lab_annotations
+    cln = @pnt.clinical.first
+    assert_not_nil(cln, "Clinical annotation not added to participant")
+    labs = cln.lab_annotations
     assert_not_nil(labs.first, "Lab not added to participant labs")
     assert_same(lab, labs.first, "Lab incorrect")
-    assert_same(@pnt, lab.owner, "Lab proxy hook not set")
+    assert_same(@pnt, lab.hook, "Lab proxy hook not set")
+  end
+  
+  def test_radiation_annotation
+    if CaTissue::Participant::Clinical::RadiationTherapy != CaTissue::Participant::Clinical::RadRXAnnotation then
+      assert_raises(CaTissue::AnnotationError, "RadiationTherapy is not deprecated.") { CaTissue::Participant::Clinical::RadiationTherapy.new}
+    end
+  end  
+
+  def test_chemotherapy_annotation
+    if CaTissue::Participant::Clinical::Chemotherapy != CaTissue::Participant::Clinical::ChemoRXAnnotation then
+      assert_raises(CaTissue::AnnotationError, "Chemotherapy is not deprecated.") { CaTissue::Participant::Clinical::Chemotherapy.new}
+    end
   end
 
+   ## DATABASE TEST CASES
+
   # Tests creating a participant.
   def test_save
     verify_save(@pnt)
@@ -72,6 +123,17 @@ class ParticipantTest < Test::Unit::TestCase
     assert_not_nil(lab.identifier, "Lab not saved")
   end
   
+  # Tests saving a participant treatment annotation. 
+  def test_save_treatment_annotation
+    trt = CaTissue::Participant::Clinical::TreatmentAnnotation.new
+    trt.merge_attributes(:agent => 'ACACIA', :participant => @pnt)
+    dur = CaTissue::Participant::Clinical::Duration.new
+    dur.merge_attributes(:start_date => DateTime.new(2010, 10, 10), :end_date => DateTime.new(2010, 12, 10), :treatment => trt)
+    verify_save(trt)
+    assert_not_nil(trt.identifier, "Treatment not saved")
+    assert_not_nil(dur.identifier, "Treatment duration not saved")
+  end
+  
   # Exercises creation of both a HealthExaminationAnnotation and a NewDiagnosisHealthAnnotation.
   # These annotation classes are both primary and share a comman ancestor entity used
   # as the basis for generating database identifiers.
@@ -86,23 +148,16 @@ class ParticipantTest < Test::Unit::TestCase
     verify_save(hdgn)
   end
   
-  def test_save_treatment_annotation
-    date = DateTime.new(2010, 10, 10)
-    trt = CaTissue::Participant::Clinical::TreatmentAnnotation.new
-    trt.merge_attributes(:other_agent => 'Radical Prostatectomy', :participant => @pnt)
-    dtn = CaTissue::Participant::Clinical::Duration.new
-    dtn.merge_attributes(:start_date => date, :end_date => date, :duration_in_days => 1, :treatment_annotation => trt)
-    verify_save(trt)
+  def test_save_radiation_annotation
+    rad = CaTissue::Participant::Clinical::RadRXAnnotation.new
+    rad.merge_attributes(:other_agent => 'Adjuvant Radiation Therapy', :participant => @pnt)
+    verify_save(rad)
   end
   
-  # caTissue alert - The RadiationTherapy DE class is not supported, since it is not a primary entity.
-  # RadRXAnnotation is used instead.  The purpose of the caTissue RadiationTherapy class is unknown,
-  # since it adds nothing to RadRXAnnotation. The same consideration applies to Chemotherapy.
-  # TODO - check with caTissue support and either request deprecation or add caRuby support.
-  def test_save_radiation_annotation
-    rdx = CaTissue::Participant::Clinical::RadRXAnnotation.new
-    rdx.merge_attributes(:other_agent => 'Adjuvant Radiation Therapy', :participant => @pnt)
-    verify_save(rdx)
+  def test_save_chemo_annotation
+    chm = CaTissue::Participant::Clinical::ChemoRXAnnotation.new
+    chm.merge_attributes(:other_agent => 'Adjuvant Chemotherapy', :participant => @pnt)
+    verify_save(chm)
   end
   
   def test_save_exam_annotation