caruby-tissue 1.5.6 → 2.1.1

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

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class SpecimenPositionTest < Test::Unit::TestCase
   include CaTissue::TestCase

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

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class SpecimenRequirementTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -27,7 +27,7 @@ class SpecimenRequirementTest < Test::Unit::TestCase
      @rqmt.derive(:count => 2, :specimen_type => (@rqmt.specimen_type + ' Block'))
      assert_equal(2, @rqmt.children.size, "Derived requirement count incorrect")
      @rqmt.add_defaults
-     assert_raise(ValidationError, "Multiple derivatives incorrectly succeeds validation") { @rqmt.validate }
+     assert_raise(Jinx::ValidationError, "Multiple derivatives incorrectly succeeds validation") { @rqmt.validate }
    end
 
   def test_save

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

@@ -1,5 +1,5 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/util/transitive_closure'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/transitive_closure'
 
 class SpecimenTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -11,8 +11,8 @@ class SpecimenTest < Test::Unit::TestCase
 
   def test_requirement_copy
     rqmt = @spc.requirement
-    rqmt.value_hash(rqmt.class.nondomain_attributes).each do |attr, value|
-      assert_equal(value, @spc.send(attr), "Specimen requirement #{attr} not copied")
+    rqmt.value_hash(rqmt.class.nondomain_attributes).each do |pa, value|
+      assert_equal(value, @spc.send(pa), "Specimen requirement #{pa} not copied")
     end
   end
 
@@ -133,7 +133,7 @@ class SpecimenTest < Test::Unit::TestCase
     end
   end
 
-  # Tests whether a Specimen with a position save template does not include the position.
+  # Tests whether a specimen with a position save template does not include the position.
   # The position is saved as a caTissue side-effect by creating a proxy transfer event.
   def test_position_save_template
     defaults.box << @spc
@@ -143,7 +143,7 @@ class SpecimenTest < Test::Unit::TestCase
     assert_nil(tmpl.position, "#{@spc.qp} save template incorrectly includes the position")
   end
 
-  def test_pathology_annotation
+  def test_prostate_annotation
     pst = CaTissue::Specimen::Pathology::ProstateSpecimenPathologyAnnotation.new
     pst.merge_attributes(:specimen => @spc)
     grade = CaTissue::Specimen::Pathology::SpecimenHistologicGrade.new
@@ -162,10 +162,9 @@ class SpecimenTest < Test::Unit::TestCase
     assert_same(htype, pst.histologic_types.first, "Prostate annotation histologic types incorrect")
   end
 
-  # Verifies that caRuby Tissue is compatible with both the caTissue 1.1 and 1.2 Specimen annotation class names. 
+  # Verifies that caRuby Tissue is compatible with both the caTissue 1.1.2 and 1.2 Specimen annotation class names. 
   def test_rename
     assert_same(CaTissue::Specimen::Pathology::SpecimenAdditionalFinding, CaTissue::Specimen::Pathology::AdditionalFinding, "caTissue 1.2 annotation class rename unsupported")
-    assert_same(CaTissue::Specimen::Pathology::SpecimenBaseSolidTissuePathologyAnnotation, CaTissue::Specimen::Pathology::SpecimenBaseSolidTissuePathologyAnnotation, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::SpecimenDetails, CaTissue::Specimen::Pathology::Details, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::ProstateSpecimenGleasonScore, CaTissue::Specimen::Pathology::GleasonScore, "caTissue 1.2 annotation class rename unsupported")
     assert_same(CaTissue::Specimen::Pathology::SpecimenHistologicGrade, CaTissue::Specimen::Pathology::HistologicGrade, "caTissue 1.2 annotation class rename unsupported")
@@ -213,21 +212,51 @@ class SpecimenTest < Test::Unit::TestCase
     assert_equal(changed, chr.tissue_site, "#{@spc} #{chr} tissue site not updated")
   end
   
-  def test_event_save
+  def test_nondisposal_specimen_event_save
     # add an event
     ev = CaTissue::SpunEventParameters.new(:specimen => @spc, :duration_in_minutes => 2, :gravity_force => 5)
     verify_save(@spc)
     assert_not_nil(ev.identifier, "#{@spc} event #{ev} not saved")
+    # make a nonanticipatory specimen
+    spc2 = CaTissue::Specimen.create_specimen(
+      :requirement => defaults.specimen_requirement,
+      :specimen_collection_group => defaults.specimen_collection_group,
+      :initial_quantity => 2.0)
+    # add an event to the nonanticipatory specimen
+    ev2 = CaTissue::SpunEventParameters.new(:specimen => spc2, :duration_in_minutes => 1, :gravity_force => 3)
+    # Save the new specimen
+    verify_save(spc2)
+    assert_not_nil(ev.identifier, "#{spc2} event #{ev2} not saved")
   end
   
-  # Tests the work-around for caTissue Bug #159: Update pending Specimen ignores availableQuantity.
+  # Verifies the caRuby Bug #9, #10 and #11 fixes.
+  def test_disposal_event_save
+    # add an event to the anticipatory specimen
+    ev = CaTissue::DisposalEventParameters.new(:specimen => @spc)
+    # Save the specimen, which will update the anticipatory specimen
+    verify_save(@spc)
+    assert_not_nil(ev.identifier, "#{@spc} event #{ev} not saved")
+    assert_equal('Closed', @spc.activity_status, "Disposed #{@spc} is not closed")
+    # Make a nonanticipatory specimen.
+    spc2 = CaTissue::Specimen.create_specimen(
+      :requirement => defaults.specimen_requirement,
+      :specimen_collection_group => defaults.specimen_collection_group,
+      :initial_quantity => 2.0)
+    # Dispose the nonanticipatory specimen.
+    ev2 = CaTissue::DisposalEventParameters.new(:specimen => spc2)
+    # Save the new disposed specimen.
+    verify_save(spc2)
+    assert_not_nil(ev2.identifier, "#{spc2} event #{ev2} not saved")
+  end
+ 
+  # Verifies the work-around for caTissue Bug #159: Update pending Specimen ignores availableQuantity.
   def test_quantity_save
     # reset the available quantity
     @spc.available_quantity = @spc.initial_quantity / 2
     verify_save(@spc)
   end
 
-  # Exercises the CaTissue::Specimen external_identifiers logical dependency work-around.
+  # Verifies the CaTissue::Specimen external_identifiers logical dependency work-around.
   def test_eid_save
     verify_save(@spc)
     # add an EID
@@ -255,12 +284,6 @@ class SpecimenTest < Test::Unit::TestCase
     logger.debug { "#{self} updating second EID specimen #{spc2}..." }
     verify_save(spc2)
   end
-   
-  def test_events_save
-    # add an event
-    CaTissue::FrozenEventParameters.new(:specimen => @spc, :freeze_method => 'Cryostat')
-    verify_save(@spc)
-  end
 
   def test_position_save
     defaults.box << @spc
@@ -271,13 +294,12 @@ class SpecimenTest < Test::Unit::TestCase
     verify_save(@spc)
   end
   
-  # Exercise creation of a child specimen.
+  # Exercises creation of a child specimen.
   def test_derived_create
-    # verify creating a derived specimen
-    logger.debug { "Verifying creating a derived specimen..." }
     # derive a specimen
     drv = @spc.derive(:specimen_class => :molecular, :initial_quantity => 20, :specimen_type => 'DNA')
-    # store the derived specimen
+    logger.debug { "#{name} verifying creation of derived specimen #{@spc}..." }
+    # save the derived specimen
     verify_save(drv)
     # verify the derived specimen parent
     assert_same(@spc, drv.parent, "Derived specimen parent incorrect after store")
@@ -288,8 +310,20 @@ class SpecimenTest < Test::Unit::TestCase
       assert(drv.match_in_owner_scope(children), "Derived specimen not found in parent query result")
     end
   end
+
+  # Exercises aliquot creation.
+  def test_aliquot_create
+    # make the aliquots
+    alqs = @spc.derive(:count => 2)
+    # save the specimens
+    verify_save(@spc)
+    # verify that each aliquot was created
+    alqs.each do |alq|
+      assert_not_nil(alq.identifier, "#{@spc} aliquot #{alq} not saved")
+    end
+  end
   
-  # Exercise update of an auto-generated child specimen.
+  # Exercises update of an auto-generated child specimen.
   #
   # This test case differs from {#test_derived_create} in that there are critical caTissue code path
   # differences which dictate how the derived object save template is built. See the caTissue
@@ -305,7 +339,7 @@ class SpecimenTest < Test::Unit::TestCase
     verify_save(drv)
   end
   
-  def test_save_prostate_annotation
+  def test_prostate_annotation_save
     pa = CaTissue::Specimen::Pathology::ProstateSpecimenPathologyAnnotation.new
     pa.specimen = @spc
     grade = CaTissue::Specimen::Pathology::SpecimenHistologicGrade.new
@@ -324,7 +358,7 @@ class SpecimenTest < Test::Unit::TestCase
     assert_not_nil(gleason.identifier, "#{gleason} not saved")
   end
 
-  def test_save_melanoma_annotation
+  def test_melanoma_annotation_save
     ma = CaTissue::Specimen::Pathology::MelanomaSpecimenPathologyAnnotation.new
     ma.merge_attributes(:specimen => @spc, :comments => "Test Comment", :depth_of_invasion => 2.0, :mitotic_index => "Less than 1 mitotic figure per mm-square",
       :ulceration => "Absent", :tumor_regression => "Present involving 75% or more of lesion", :tumor_infiltrating_lymphocytes => "Brisk")

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

@@ -1,5 +1,5 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/util/uniquifier'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/uniquifier'
 
 class StorageContainerTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -104,19 +104,6 @@ class StorageContainerTest < Test::Unit::TestCase
     assert(@frz.completely_full?, "Freezer incorrectly not completely full")
   end
 
-  def test_comparison
-    @frz << @spc
-    assert_equal(@frz, @frz, "Same not equal")
-    rack = @frz.subcontainers.first
-    assert_not_nil(rack, "Rack missing")
-    box = rack.subcontainers.first
-    assert_not_nil(box, "Box missing")
-    assert(rack < @frz, "Rack not < freezer")
-    assert(@frz > rack, "Freezer not > rack")
-    assert(box < rack, "Box not < rack")
-    assert(box < @frz, "Box not < rack")
-  end
-
   def test_save
     @frz << @spc
     rack = @frz.subcontainers.first
@@ -148,4 +135,4 @@ class StorageContainerTest < Test::Unit::TestCase
     assert_not_nil(@spc.identifier, "#{@spc} not saved")
     assert_not_nil(@spc.position, "#{@spc} missing position")
   end
-end
+end

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

@@ -1,5 +1,5 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/util/uniquifier'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/uniquifier'
 
 class StorageTypeTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -66,4 +66,4 @@ class StorageTypeTest < Test::Unit::TestCase
     stored = @box_type.find_containers.map { |ctr| ctr.identifier}
     assert_equal([box.identifier], stored, "Box with identifier #{box.identifier} not found")
   end
-end
+end

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

@@ -1,5 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/database/store_template_builder'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class TransferEventParametersTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -14,26 +13,27 @@ class TransferEventParametersTest < Test::Unit::TestCase
   def test_defaults
     verify_defaults(@xfr)
   end
+  
+  def test_match
+    other = @xfr.copy
+    assert(!@xfr.matches?(other), "#{other} incorrectly matches #{@xfr}")
+  end
 
   def test_inverse_setter
-    assert(@xfr.specimen.event_parameters.include?(@xfr), "EventParameters not found in specimen")
+    assert(@xfr.specimen.event_parameters.include?(@xfr), "#{@xfr} not found in specimen")
   end
 
-  def test_save
-    logger.debug { "#{self} testing #{xfr.specimen} storage at #{xfr.to.coordinate.qp}." }
-    verify_save(@xfr)
-    shift(@xfr)
-    logger.debug { "#{self} testing #{xfr.specimen} move from #{xfr.from.coordinate.qp} to #{xfr.to.coordinate.qp}." }
-    verify_save(@xfr)
+  def test_move
+    prev = @xfr.to
+    @xfr.to = prev.succ
+    assert_equal(prev.column + 1, @xfr.to.column, "#{@xfr} position not incremented")
   end
 
-  private
-
-  # Resets the given CaTissue::TransferEventParameters xfr so that +from+ is the
-  # old +to+, +to+ is the next location, and the identifier is cleared.
-  def shift(xfr)
-    xfr.from = xfr.to
-    xfr.to = xfr.from.succ
-    xfr.identifier = nil
+  def test_save
+    logger.debug { "#{self} testing #{@xfr.specimen} storage at #{@xfr.to.coordinate.qp}." }
+    verify_save(@xfr)
+    moved = CaTissue::TransferEventParameters.new(:specimen => @xfr.specimen, :from => @xfr.to, :to => @xfr.to.succ)
+    logger.debug { "#{self} testing #{@xfr.specimen} move from #{moved.from.coordinate.qp} to #{moved.to.coordinate.qp}." }
+    verify_save(moved)
   end
 end

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

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class UserTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -8,42 +8,40 @@ class UserTest < Test::Unit::TestCase
     @user = defaults.tissue_bank.coordinator
   end
 
-#  # Verifies the secondary key.
-#  def test_secondary_key
-#    assert_equal(@user.login_name, @user.key, 'Key incorrect')
-#  end
-#
-#  def test_defaults
-#    verify_defaults
-#  end
-#
-#  # Exercises setting the login name from the email address.
-#  def test_default_login_value
-#    @user.login_name = nil
-#    verify_defaults
-#  end
-#
-#  # Exercises setting the email address from the login name.
-#  def test_default_email_value
-#    @user.email_address = nil
-#    verify_defaults
-#  end
-#
-#  def verify_defaults
-#    @user.address.identifier = 1
-#    @user.cancer_research_group.identifier = 2
-#    @user.department.identifier = 3
-#    @user.institution.identifier = 4
-#    super(@user)
-#  end
+  # Verifies the secondary key.
+  def test_secondary_key
+    assert_equal(@user.login_name, @user.key, 'Key incorrect')
+  end
+
+  def test_defaults
+    verify_defaults(@user)
+  end
 
-  # Tests creating a user.
+  # Exercises setting the login name from the email address.
+  def test_default_login_value
+    @user.login_name = nil
+    verify_defaults(@user)
+  end
+
+  # Exercises setting the email address from the login name.
+  def test_default_email_value
+    @user.email_address = nil
+    verify_defaults(@user)
+  end
+
+  # Tests creating a user and updating the address.
   def test_save
-    addr = @user.email_address
-    at_ndx = addr.index('@')
-    modifier = "_#{Uniquifier.qualifier.to_s}"
-    @user.email_address = addr.insert(at_ndx, modifier)
+    # Create the user with a unique email.
+    email = @user.email_address
+    at_ndx = email.index('@')
+    modifier = "_#{Jinx::Uniquifier.qualifier}"
+    @user.email_address = email.insert(at_ndx, modifier)
     @user.login_name = nil
     verify_save(@user)
+    
+    # Update the address.
+    logger.debug { "#{self} updating the #{@user} address..." }
+    @user.address.street = "#{Jinx::Uniquifier.qualifier} Elm St."
+    verify_save(@user)
   end
 end

data/test/lib/catissue/helpers/properties_loader_test.rb

@@ -0,0 +1,19 @@
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+
+# This class verifies that the classpath property is loaded or inferred.
+# Manually verify that the classpath is inferred by removing the
+# +~/.catissue+ file and setting the +CATISSUE_CLIENT_HOME+ env var.
+class PropertiesLoaderTest < Test::Unit::TestCase
+  def setup
+    # the path before loading caTissue
+    before = $CLASSPATH.to_s
+    # Induce application property load by referencing the properties.
+    CaTissue::Specimen
+    # the difference between the path before and after loading caTissue
+    @path = $CLASSPATH.to_s[before.length..-1]
+  end
+  
+  def test_path
+    assert_not_nil(@path, "path property was not loaded")
+  end
+end

data/test/lib/catissue/migration/{test_case.rb → helpers/test_case.rb}

@@ -1,7 +1,5 @@
-LOG_FILE = 'test/results/log/migration.log'
-
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/domain/uniquify'
+require File.dirname(__FILE__) + '/../../../../helpers/test_case'
+require 'jinx/helpers/uniquifier'
 require 'catissue/migration/migrator'
 
 module CaTissue
@@ -10,23 +8,29 @@ module CaTissue
 
     #@param [String] fixtures the fixtures directory
     def setup(fixtures)
+      super()
       @fixtures = fixtures
       # Clear the uniquifier for this migration.
-      CaRuby::ResourceUniquifier.instance.clear
+      Jinx::Uniquifier.instance.clear
     end
 
-    ## MIGRATION TEST UTILITY METHODS ##
-
     private
 
+    # @group Migration test utility methods
+
     # Runs a migrator on the given input fixture and options.
     #
     # @param (see #create_migrator)
     # @option (see #create_migrator)
-    def migrate_to_database(fixture, opts={}, &verifier)
+    # @yield [obj] verify the migration
+    # @yieldparam [Resource] obj the migrated object
+    def migrate_to_database(fixture, opts={})
       mgtr = create_migrator(fixture, opts)
       logger.debug { "Migration test migrating #{fixture} fixture..." }
-      mgtr.migrate_to_database(&verifier)
+      mgtr.migrate_to_database do |tgt, rec|
+        @post_pcsr.call(tgt) if @post_pcsr
+        yield tgt if block_given?
+      end
       logger.debug { "Migration test migrated #{fixture} fixture." }
     end
 
@@ -34,24 +38,26 @@ module CaTissue
     # If a factory block is provided, then that factory is called to make a new
     # Migrator instance. Otherwise, {CaTissue::Migrator#initialize} makes the instance.
     #
-    # If there is no :input option, then the migration input is set to the
+    # If there is no +:input+ option, then the migration input is set to the
     # _fixture_.+csv+ file in the {#initialize} fixtures directory.
     #
     # @param [Symbol] fixture the migration test fixture
     # @param [{Symbol => Object}] opts (see CaTissue::Migrator#initialize)
     # @option (see CaTissue::Migrator#initialize)
+    # @yield [obj] post-process the migrated object
+    # @yieldparam [Resource] obj the migrated object
     # @return [CaTissue::Migrator]
-    # @yield [opts] the optional Migrator factory
-    def create_migrator(fixture, opts={}, &factory)
-      opts[:input] ||= File.join(@fixtures, fixture.to_s + '.csv')
-      block_given? ? yield(opts) : CaTissue::Migrator.new(opts)
+    def create_migrator(fixture, opts={}, &block)
+      opts[:input] ||= File.expand_path("#{fixture}.csv", @fixtures)
+      @post_pcsr = block if block_given?
+      CaTissue::Migrator.new(opts)
     end
 
     # Verifies that the given test fixture is successfully migrated.
     # Each migrated target object is validated using {CaTissue::TestCase#verify_saved}.
     # In addition, if a verifier block is given to this method, then that block is
     # called on the target migration object, or nil if no target was migrated.
-    # Supported options are described in {CaTissue::Migrator#migrate}.
+    # Supported options are described in +Jinx::Migrator.migrate+.
     #
     # @param (see #verify_target)
     # @option (see #verify_target)
@@ -60,8 +66,8 @@ module CaTissue
     def verify_save(fixture, opts={})
       logger.debug { "Migrating the #{fixture} test fixture..." }
       opts[:unique] = true unless opts.has_key?(:unique)
-      opts[:controlled_values] = true unless opts.has_key?(:controlled_values)
-      migrate_to_database(fixture, opts) do |tgt|
+      migrate_to_database(fixture, opts) do |tgt, rec|
+        @post_pcsr.call(tgt) if @post_pcsr
         verify_saved(tgt)
         yield tgt if block_given?
       end
@@ -70,6 +76,7 @@ module CaTissue
     # Verifies the given fixture migration.
     # Each migrated target object is validated using {#validate_target}.
     # The target is migrated but not stored.
+    # The +:unique+ option is set to false by default.
     #
     # @param [Symbol] fixture the test fixture to verify
     # @param [<Symbol>] opts the migration options
@@ -78,7 +85,10 @@ module CaTissue
     # @yieldparam [Resource] target the domain object to verify
     def verify_target(fixture, opts={}, &verifier)
       opts[:unique] ||= false
-      create_migrator(fixture, opts).migrate { |tgt| validate_target(tgt, &verifier) }
+      create_migrator(fixture, opts).migrate do |tgt, rec|
+        @post_pcsr.call(tgt) if @post_pcsr
+        validate_target(tgt, &verifier)
+      end
     end
 
     # Validates that the given target was successfully migrated.
@@ -93,10 +103,10 @@ module CaTissue
     def validate_target(target)
       assert_not_nil(target, "Missing target")
       logger.debug { "Validating migration target #{target}..." }
-      verify_defaults(target) if target
+      verify_defaults(target) unless target.identifier
       yield target if block_given?
       logger.debug { "Validated migration target #{target}." }
       target
     end
   end
-end
+end