caruby-tissue 1.3.1 → 1.3.2

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

@@ -0,0 +1,30 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class SiteTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @site = defaults.tissue_bank
+    @site.name = @site.name.uniquify
+  end
+
+  def test_defaults
+    verify_defaults(@site)
+  end
+
+  def test_save
+    # create the site
+    verify_save(@site)
+    # modify the site address; this changes the existing address rather than creating a new address
+    identifier = @site.address.identifier
+    zip_code = @site.address.zip_code = @site.address.zip_code.to_i + 1
+    verify_save(@site)
+    # clear the address identifier zip code and refetch the site; this sets the zip code to the database value
+    @site.address.identifier = @site.address.zip_code = nil
+    database.find(@site)
+    assert_equal(zip_code, @site.address.zip_code.to_i, "Updated zip code incorrect.")
+    assert_equal(identifier, @site.address.identifier, "Address replaced rather than updated.")
+  end
+end

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

@@ -0,0 +1,38 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class SpecimenArrayTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @spc = defaults.specimen
+    array_type = CaTissue::SpecimenArrayType.new(:name => 'SpecimenArray'.uniquify, :specimen_class => @spc.specimen_class,
+      :specimen_types => [@spc.specimen_type], :columns => 5, :rows => 5)
+    @array = CaTissue::SpecimenArray.new(:container_type => array_type)
+  end
+
+  def test_defaults
+    verify_defaults(@array)
+  end
+  
+  def test_occupied_positions_occlusion
+    assert(!CaTissue::SpecimenArray.attributes.include?(:occupied_positions), "occupied_positions is not excluded from SpecimenArray")
+    assert(CaTissue::Container.attributes.include?(:occupied_positions), "occupied_positions is not retained in the SpecimenArray superclass")
+  end
+
+  def test_can_hold_type
+    assert(@array.can_hold_child?(@spc), "Array can't hold specimen type")
+    @spc.specimen_type = 'Fixed Tissue'
+    assert(!@array.can_hold_child?(@spc), "Array can't hold different specimen type")
+  end
+  
+  def test_add
+    assert_raises(NotImplementedError, "Specimen position specimen incorrect") { @array << @spc }
+  end
+
+#  def test_save
+#    verify_save(@array)
+#  end
+end

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

@@ -0,0 +1,27 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+
+class SpecimenArrayTypeTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @type = CaTissue::SpecimenArrayType.new(:name => 'SpecimenArrayType'.uniquify,
+      :specimen_class => 'Frozen Tissue', :columns => 5,  :rows => 5)
+    @type.specimen_types << 'Tissue'
+  end
+
+  def test_defaults
+    verify_defaults(@type)
+  end
+
+  def test_create
+    array = @type.create
+    assert_same(CaTissue::SpecimenArray, array.class, "Created instance class incorrect")
+    assert_same(@type, array.container_type, "Created array type incorrect")
+  end
+
+  def test_save
+    verify_save(@type)
+  end
+end

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

@@ -0,0 +1,15 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class SpecimenCharacteristicsTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @chr = defaults.specimen_requirement.characteristics
+  end
+
+  def test_defaults
+    verify_defaults(@chr)
+  end
+end

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

@@ -0,0 +1,216 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class SpecimenCollectionGroupTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @scg = defaults.specimen_collection_group
+  end
+
+  # This test case exercises the key method for a domain class with a secondary key.
+  def test_secondary_key
+    @scg.name = 'Test SCG'
+    assert_equal(@scg.name, @scg.key, 'Key incorrect')
+  end
+
+  def test_defaults
+    verify_defaults(@scg)
+    assert_equal('Complete', @scg.collection_status, "SCG collection status default incorrect")
+    @scg.registration.consent_tier_responses.each do |ctr|
+      ct = ctr.consent_tier
+      cts = @scg.consent_tier_statuses.detect { |s| s.consent_tier == ct }
+      assert_not_nil(cts, "Missing SCG consent tier status for #{ct}")
+    end
+  end
+
+  def test_default_collection_event
+    collection_event = @scg.collection_event
+    @scg.collection_event = nil
+    assert_nil(@scg.collection_event, 'Collection event not removed')
+    @scg.add_defaults
+    assert_equal(collection_event, @scg.collection_event, 'Collection event not set to default')
+  end
+
+  def test_base_haematology_pathology
+    scg = CaTissue::SpecimenCollectionGroup.new
+    pths = scg.radical_prostatectomy_pathology_annotations
+    assert(pths.empty?, "Prostatectomy annotations not empty at start")
+    pth = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.new
+    pth.merge_attributes(:specimen_procedure => 'Biopsy', :specimen_collection_group => scg)
+    epx = CaTissue::SpecimenCollectionGroup::Pathology::ExtraprostaticExtension.new
+    epx.merge_attributes(:status => 'Present', :radical_prostatectomy_pathology_annotation => pth)
+    pths = scg.radical_prostatectomy_pathology_annotations
+    assert_not_nil(pths.first, "Prostatectomy annotation not added to #{scg} annotations")
+    assert_same(pth, pths.first, "Prostatectomy annotation incorrect")
+    assert_same(scg, pth.owner, "Prostatectomy annotation proxy hook not set")
+    assert_not_nil(pth.extraprostatic_extension, "#{pth} extraprostatic extension not set")
+    assert_same(epx, pth.extraprostatic_extension, "{pth} extraprostatic extension incorrect")
+  end
+
+  def test_collect
+    scg = CaTissue::SpecimenCollectionGroup.new
+    cdt = DateTime.now
+    scg.collect(:collector => @scg.collector, :collection_date => cdt, :receiver => @scg.receiver)
+    assert_not_nil(scg.collection_event_parameters, "Collected SCG missing collection event parameters")
+    assert_same(@scg.collector, scg.collection_event_parameters.user, "SCG collector incorrect")
+    assert_equal(cdt.to_s, scg.collection_event_parameters.timestamp.to_s, "SCG collection time incorrect")
+    assert_not_nil(scg.received_event_parameters, "Received SCG missing received event parameters")
+    assert_same(@scg.receiver, scg.received_event_parameters.user, "SCG receiver incorrect")
+    assert_equal(cdt.to_s, scg.received_event_parameters.timestamp.to_s, "SCG received time not defaulted to collection time")
+  end
+
+  def test_save
+    logger.debug { "Verifying SCG create..." }
+    verify_save(@scg)
+    assert_equal('Complete', @scg.collection_status, "Collection status after store incorrect")
+    assert_equal(2, @scg.events.size, "#{@scg} events size incorrect")
+    tmpl = @scg.copy(:identifier)
+    verify_query(tmpl, :events) do |fetched|
+      assert_equal(2, fetched.size, "#{@scg} fetched events size incorrect")
+    end
+    assert_equal(1, @scg.specimens.size, "#{@scg} specimens size incorrect")
+    spc = @scg.specimens.first
+    assert_equal(2, spc.events.size, "#{@scg} #{spc} events size incorrect")
+    verify_query(spc, :events) do |fetched|
+      assert_equal(2, fetched.size, "#{@scg} #{spc} events query result size incorrect")
+    end
+
+    # test update
+    @scg.diagnosis = 'Pleomorphic carcinoma'
+    # set an event comment
+    cep = @scg.specimen_event_parameters.detect { |param| CaTissue::CollectionEventParameters === param }
+    cep.comment = 'Test Comment'
+    verify_save(@scg)
+
+    # query the specimens
+    logger.debug { "Verifying #{@scg.qp} specimens query..." }
+    tmpl = @scg.copy(@scg.class.secondary_key_attributes)
+    verify_query(tmpl, :specimens) do |fetched|
+      assert_equal(1, fetched.size, "#{@scg} specimens query result size incorrect")
+      spc = fetched.first
+      assert_equal(@scg.specimens.first.identifier, spc.identifier, "#{@scg} fetched #{spc} identifier incorrect")
+    end
+
+    # query the collection event parameters
+    logger.debug { "Verifying that #{@scg.qp} specimen_event_parameters are created..." }
+    verify_query(tmpl) do |fetched|
+      assert_equal(@scg.specimen_event_parameters.size, fetched.first.specimen_event_parameters.size, "Event query result size incorrect")
+      # the fetched CEP
+      fcep = fetched.first.specimen_event_parameters.detect { |param| CaTissue::CollectionEventParameters === param }
+      assert_not_nil(fcep, "Collection event missing")
+      assert_equal('Test Comment', fcep.comment, "Collection event comment not saved")
+    end
+
+    # update the comment
+    logger.debug { "Verifying #{@scg.qp} update..." }
+    @scg.comment = comment = 'Test Comment'
+    verify_save(@scg)
+    @scg.comment = nil
+    database.find(@scg)
+    assert_equal(comment, @scg.comment, "Comment not updated in database")
+    logger.debug { "Verified #{@scg.qp} store." }
+
+    # create a new SCG with two specimens
+    logger.debug { "Verifying second SCG create..." }
+    cpe = @scg.collection_event
+    rcvr = defaults.tissue_bank.coordinator
+    reg = @scg.registration
+    pnt = reg.participant
+    pcl = reg.protocol
+    rqmt = defaults.specimen_requirement
+    spc1 = CaTissue::Specimen.create_specimen(:requirement => rqmt, :initial_quantity => 1.0)
+    spc2 = CaTissue::Specimen.create_specimen(:requirement => rqmt, :initial_quantity => 1.0)
+    site = defaults.tissue_bank
+    scg = pcl.add_specimens(spc1, spc2, :participant => pnt, :site => site, :collection_event => cpe, :receiver => rcvr)
+    verify_save(scg)
+    spcs = scg.query(:specimens)
+    spc_ids = spcs.map { |spc| spc.identifier }
+    assert_equal(2, spcs.size, "#{scg} specimens size incorrect")
+    assert(spc_ids.include?(spc1.identifier), "#{scg} specimen #{spc1} not found")
+    assert(spc_ids.include?(spc2.identifier), "#{scg} specimen #{spc2} not found")
+  end
+
+  # This test follows caTissue SCG, SEP and Specimen auto-generation as follows:
+  # * Create CPR => SCG auto-generated with status Pending, new Specimen, no SCG SEP
+  # * Update SCG status to Complete => SCG SEP created
+  def test_autogenerated
+    # make a new registration
+    pnt = CaTissue::Participant.new(:name => 'Test Participant'.uniquify)
+    pcl = defaults.protocol
+    cpr = pcl.register(pnt)
+
+    # store the registration without an SCG
+    verify_save(cpr)
+    # the auto-generated SCG
+    scg = cpr.specimen_collection_groups.first
+    assert_not_nil(scg, "Missing auto-generated SCG")
+    assert_not_nil(scg.identifier, "Auto-generated SCG missing identifier")
+    assert_not_nil(scg.collection_event, "Auto-generated SCG missing collection event")
+    assert_equal('Pending', scg.collection_status, "Auto-generated SCG status is not Pending")
+    # the auto-generated Specimen
+    spc = scg.specimens.first
+    assert_not_nil(spc, "Auto-generated specimen was not fetched")
+    # SEP is not auto-generated
+    assert(scg.specimen_event_parameters.empty?, "SEP unexpectedly auto-generated")
+    # auto-generated SCG does not have a site, even though it is required for create or update
+    assert_nil(scg.collection_site, "SCG collection site unexpectedly auto-generated")
+
+    # update the SCG with site and SEPs
+    rcvr = defaults.tissue_bank.coordinator
+    site = defaults.specimen_collection_group.collection_site
+    scg.merge_attributes(:receiver => rcvr, :collection_site => site).add_defaults
+    logger.debug { "#{self.class.qp} updating the auto-generated #{scg.qp}..." }
+    scg.update
+    # clear and refetch the status
+    scg.collection_status = nil
+    logger.debug { "#{self.class.qp} refetching the updated #{scg.qp}..." }
+    scg.find
+    assert_equal('Pending', spc.collection_status, "Auto-generated specimen status is not Pending after update")
+
+    # reset some specimen fields and update
+    spc.collection_status = 'Collected'
+    spc.specimen_type = 'Frozen Tissue'
+    spc.initial_quantity = 0.1
+    spc.specimen_characteristics.tissue_site = 'Ileum'
+    logger.debug { "#{self.class.qp} updating auto-generated #{spc.qp}..." }
+    verify_save(spc)
+
+    # clear and refetch some specimen fields
+    spc.collection_status = nil
+    spc.specimen_characteristics.tissue_site = nil
+    logger.debug { "#{self.class.qp} verifying the persistent state of the updated #{scg.qp} auto-generated specimen..." }
+    database.find(spc)
+    assert_equal('Collected', spc.collection_status, "Specimen status not updated")
+    assert_equal('Ileum', spc.specimen_characteristics.tissue_site, "Specimen tissue site not updated")
+
+    # update the SCG with complete status
+    scg.collection_status = 'Complete'
+    logger.debug { "#{self.class.qp} updating the #{scg.qp} collection status #{scg.qp}..." }
+    scg.update
+    verify_save(scg)
+  end
+  
+  def test_save_prostate_annotation
+    pa = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyPathologyAnnotation.new
+    pa.specimen_collection_group = @scg
+    htype = CaTissue::SpecimenCollectionGroup::Pathology::HistologicType.new
+    htype.merge_attributes(:type => 3, :base_pathology_annotation => pa)
+    grade = CaTissue::SpecimenCollectionGroup::Pathology::HistologicGrade.new
+    grade.merge_attributes(:grade => 3, :base_solid_tissue_pathology_annotation => pa)
+    invn = CaTissue::SpecimenCollectionGroup::Pathology::Invasion.new
+    invn.merge_attributes(:lymphatic_invasion => 'Present', :base_solid_tissue_pathology_annotation => pa)
+    gleason = CaTissue::SpecimenCollectionGroup::Pathology::GleasonScore.new
+    gleason.merge_attributes(:primary_pattern_score => 3, :secondary_pattern_score => 4, :prostate_pathology_annotation => pa)
+    margin = CaTissue::SpecimenCollectionGroup::Pathology::RadicalProstatectomyMargin.new
+    margin.merge_attributes(:margin_status => 'Benign glands at surgical Margin', :radical_prostatectomy_pathology_annotation => pa)
+    verify_save(pa)
+    assert_not_nil(pa.identifier, "#{@scg} annotation #{pa} not saved")
+    assert_not_nil(htype.identifier, "#{@scg} annotation #{htype} not saved")
+    assert_not_nil(grade.identifier, "#{@scg} annotation #{grade} not saved")
+    assert_not_nil(invn.identifier, "#{@scg} annotation #{invn} not saved")
+    assert_not_nil(gleason.identifier, "#{@scg} annotation #{gleason} not saved")
+    assert_not_nil(margin.identifier, "#{@scg} annotation #{margin} not saved")
+  end
+end

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

@@ -0,0 +1,61 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'catissue/defaults_test_fixture'
+
+class SpecimenEventParametersTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    specimen = defaults.specimen
+    @sep = CaTissue::SpecimenEventParameters.create_parameters(:frozen, specimen, :user => specimen.specimen_collection_group.receiver, :freeze_method => 'Cryobath')
+  end
+
+  def test_defaults
+    verify_defaults(@sep)
+  end
+
+  def test_missing_scg
+    @sep.specimen_collection_group = nil
+    assert_raises(ValidationError, "Parameters without SCG passes SCG validation") { @sep.validate }
+  end
+
+  def test_java_date
+    @sep.timestamp = now = Java.now
+    verify_defaults(@sep)
+    assert_equal(now.to_ruby_date.to_s, @sep.timestamp.to_s, "Java timestamp incorrect")
+  end
+
+  def test_ruby_date
+    @sep.timestamp = now = DateTime.now
+    verify_defaults(@sep)
+    assert_equal(now.to_s, @sep.timestamp.to_s, "Ruby timestamp incorrect")
+  end
+
+  def test_owner
+    assert_same(@sep.specimen, @sep.owner, "Specimen SEP owner incorrect")
+  end
+  
+  ## DATABASE TESTS ##
+
+  def test_scg_event_parameters_update
+    scg = @sep.specimen.specimen_collection_group
+    assert_nothing_raised("SCG not created") { database.create(scg) }
+    logger.debug { "Finding autogenerated #{scg.qp} CEP..." }
+    cep = scg.collection_event_parameters
+    assert_not_nil(cep, "Autogenerated CEP not found")
+    assert_not_nil(cep.identifier, "Autogenerated CEP identifier not set")
+    cep.collection_procedure = 'Lavage'
+    logger.debug { "Updating autogenerated #{scg.qp} CEP #{cep}..." }
+    verify_save(cep)
+  end
+
+  def test_specimen_event_parameters_create
+    verify_save(@sep)
+    tmpl = @sep.copy(:identifier)
+    logger.debug { "Verifying updated #{@sep} user fetch..." }
+    assert_not_nil(@sep.user, "User not found")
+    # update the parameters
+    @sep.freeze_method = 'Cryostat'
+    verify_save(@sep)
+  end
+end

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

@@ -0,0 +1,62 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class SpecimenPositionTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    spc = defaults.specimen
+    ctr = defaults.box
+    @pos = CaTissue::SpecimenPosition.new(:specimen => spc, :container => ctr, :column => 0, :row => 0)
+  end
+
+  def test_defaults
+    verify_defaults(@pos)
+  end
+
+  def test_inverse_setter
+    assert_same(@pos, @pos.specimen.position, "Specimen position not set")
+  end
+
+  # Tests creation of {CaTissue::TransferEventParameters} save proxy.
+  def test_saver_proxy
+    proxy = @pos.saver_proxy
+    assert_nil(proxy.from_row, "#{@pos.qp} proxy from row incorrectly set")
+    assert_nil(proxy.from_column, "#{@pos.qp} proxy from column incorrectly set")
+    assert_equal(@pos.row, proxy.to_row, "#{@pos.qp} proxy to row incorrect")
+    assert_equal(@pos.column, proxy.to_column, "#{@pos.qp} proxy to column incorrect")
+    
+    # simulate move
+    @pos.take_snapshot
+    @pos.location = @pos.location.succ
+    proxy = @pos.saver_proxy
+    assert_not_nil(proxy.from_row, "#{@pos.qp} move proxy from row not set")
+    assert_equal(@pos.snapshot[:position_dimension_one], proxy.from_position_dimension_one, "#{@pos.qp} move proxy from row incorrect")
+    assert_not_nil(proxy.to_row, "#{@pos.qp} move proxy to row not set")
+    assert_equal(@pos.snapshot[:position_dimension_two], proxy.from_position_dimension_two, "#{@pos.qp} move proxy from column incorrect")
+    assert_equal(@pos.row, proxy.to_row, "#{@pos.qp} proxy to row incorrect")
+    assert_equal(@pos.column, proxy.to_column, "#{@pos.qp} proxy to column incorrect")
+  end
+
+  def test_save
+    spc = @pos.specimen
+    verify_save(@pos)
+    assert_not_nil(spc.position, "Specimen position missing after position store")
+    assert_same(spc, @pos.specimen, "Stored position specimen differs from prior specimen")
+    assert_same(@pos, spc.position, "Specimen position differs from stored position")
+    # increment the position
+    newloc = @pos.location.succ
+    spc.move_to(newloc)
+    # verify that a specimen update also updates the position
+    logger.debug { "Verifying that specimen update reflects the position change..." }
+    spc.update
+    newpos = spc.position
+    assert_not_nil(newpos.identifier, "Specimen update did not save the new position #{newpos}")
+    verify_query(newpos.copy(:identifier)) do |result|
+      fetched = result.first
+      assert_not_nil(fetched, "New position #{newpos} could not be fetched")
+      assert_equal(newloc.coordinate, fetched.location.coordinate, "Location not updated")
+    end
+  end
+end