caruby-tissue 1.3.1 → 1.3.2

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

@@ -0,0 +1,25 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class CollectionProtocolEventTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @evt = defaults.specimen_collection_group.collection_event
+  end
+
+  def test_defaults
+    @evt.protocol.identifier = 1
+    verify_defaults(@evt)
+  end
+
+  def test_protocol_membership
+    assert(@evt.protocol.collection_protocol_events.include?(@evt), "Event not a member of its protcol events collection")
+  end
+
+  # Tests creating a protocol event.
+  def test_save
+    verify_save(@evt)
+  end
+end

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

@@ -0,0 +1,71 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class CollectionProtocolRegistrationTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @reg = defaults.registration
+  end
+
+  def test_defaults
+    verify_defaults(@reg)
+  end
+
+  def test_missing_ppi_defaults
+    @reg.protocol_participant_identifier = nil
+    verify_defaults(@reg)
+  end
+
+  def test_inverse_protocol
+    assert(@reg.protocol.registrations.include?(@reg), "Registration not included in protocol registrations")
+  end
+
+  # Tests whether the registration date can be set to either a Ruby or a Java Date and always return a Ruby Date.
+  def test_registration_date
+    value = DateTime.now
+    @reg.registration_date = value
+    assert_equal(value.to_s, @reg.registration_date.to_s, "Registration date incorrect")
+  end
+
+  def test_numeric_identifier
+    @reg.protocol_participant_identifier = 1
+    assert_equal("1", @reg.protocol_participant_identifier)
+  end
+
+  def test_disable
+    # add a derived specimen
+    specimen = @reg.specimens.first
+    child = specimen.derive(:specimen_class => :molecular, :specimen_requirement => defaults.specimen_requirement)
+    attributes = [:specimen_collection_groups, :specimens, :child_specimens]
+    @reg.visit_path(attributes) { |obj| obj.activity_status = 'Disabled' }
+    assert_equal('Disabled', @reg.activity_status, "Registration not disabled")
+    @reg.specimen_collection_groups.each { |scg| assert_equal('Disabled', scg.activity_status, "SCG #{scg} not disabled") }
+    @reg.specimens.each { |spc| assert_equal('Disabled', spc.activity_status, "Specimen #{spc} not disabled") }
+    assert_equal('Disabled', child.activity_status, "Child Specimen #{child} not disabled")
+  end
+
+  # Tests creating and fetching a registration.
+  def test_save
+    # store the registration without an SCG
+    @reg.specimen_collection_groups.clear
+    verify_save(@reg)
+
+    # an SCG should be auto-generated
+    scg = @reg.specimen_collection_groups.first
+    assert_not_nil(scg, "Missing auto-generated SCG")
+    # the SCG status is pending
+    assert_equal('Pending', scg.collection_status, "Auto-generated SCG collection status incorrect")
+
+    # modify the consent status and update
+    rsps = @reg.consent_tier_responses
+    assert_equal(1, rsps.size, "Consent tier responses size incorrect")
+    rsp = rsps.first
+    rsp.response = 'No'
+    # clear the CPR SCGs since CPR response change propagates to SCG consent status on create,
+    # which results in a test validation mismatch
+    @reg.specimen_collection_groups.clear
+    verify_save(@reg)
+  end
+end

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

@@ -0,0 +1,69 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class CollectionProtocolTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @pcl = defaults.protocol
+  end
+
+  def test_defaults
+    verify_defaults(@pcl)
+  end
+
+  # Tests the hash override.
+  def test_hash
+    hash = @pcl.hash
+    map = {@pcl => true}
+    @pcl.identifier = 1
+    assert_equal(hash, @pcl.hash, "Protocol identifier assignment changed hash")
+    assert(map[@pcl], "Protocol hash key inoperative")
+  end
+
+  def test_alias
+    assert(CaTissue::CollectionProtocol.method_defined?(:events), "Study alias not recogized: events")
+  end
+
+  # Tests the work-around for caTissue bug - CollectionProtocol and CollectionProtocolEvent are equal in caTissue 1.1.
+  def test_equals
+    assert_not_equal(@pcl, CaTissue::CollectionProtocolEvent.new, "Protocol incorrectly equals a CollectionProtocolEvent")
+  end
+
+  # Tests whether the child_collection_protocols domain type is inferred from the Java parameterized generic type property.
+  def test_assigned_protocol_users_type
+    assert_equal(CaTissue::User, @pcl.class.domain_type(:assigned_protocol_users), "assigned_protocol_users domain type incorrect")
+  end
+
+  def test_add_specimens
+    spc1 = CaTissue::TissueSpecimen.new
+    spc2 = CaTissue::TissueSpecimen.new
+    pnt = CaTissue::Participant.new(:name => 'Test Participant')
+    rcvr = CaTissue::User.new(:login_name => 'test_coordinator@example.edu')
+    site = CaTissue::Site.new(:name => 'Test Site')
+    scg = @pcl.add_specimens(spc1, spc2, :participant => pnt, :receiver => rcvr, :collection_site => site)
+    assert_equal(2, scg.size, "Specimen group size incorrect")
+    assert_equal(2, scg.specimen_event_parameters.size, "Specimen event parameters size incorrect")
+    assert_not_nil(scg.registration, "Specimen not registered")
+    assert_equal(2, @pcl.specimens(pnt).size, "Protocol specimens size incorrect")
+    assert(@pcl.specimens(pnt).include?(spc1), 'Specimen not found')
+    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")
+    event_cnt = @pcl.events.size
+    @pcl.events << event
+    assert_equal(event_cnt, @pcl.events.size, "Protocol events has duplicate event")
+  end
+
+  def test_save
+    # ignore registrations
+    @pcl.collection_protocol_registrations.clear
+    # create the protocol
+   verify_save(@pcl)
+  end
+end

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

@@ -0,0 +1,29 @@
+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
+    site = defaults.tissue_bank
+    frz_type = CaTissue::StorageType.new(:name => 'Freezer'.uniquify, :columns => 2, :rows => 1)
+    rack_type = CaTissue::StorageType.new(:name => 'Rack'.uniquify, :columns => 1, :rows => 2)
+    frz_type << rack_type
+    freezer = CaTissue::StorageContainer.new(:site => site, :container_type => frz_type)
+    rack = CaTissue::StorageContainer.new(:site => site, :container_type => rack_type)
+    @pos = CaTissue::ContainerPosition.new(:holder => freezer, :occupant => rack, :column => 0, :row => 0)
+  end
+
+  def test_defaults
+    verify_defaults(@pos)
+  end
+
+  def test_inverse_setter
+    assert_same(@pos, @pos.occupant.position, "Container position not set")
+  end
+
+  def test_save
+    verify_save(@pos)
+  end
+end

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

@@ -0,0 +1,21 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+
+class CaTissueDepartmentTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  attr_reader :department
+
+  def setup
+    super
+    @department = CaTissue::Department.new(:name => 'Test Department'.uniquify)
+  end
+
+  def test_defaults
+    verify_defaults(department)
+  end
+
+  def test_save
+    verify_save(department)
+  end
+end

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

@@ -0,0 +1,16 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'catissue/defaults_test_fixture'
+
+class DisposalEventParametersTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    specimen = defaults.specimen
+    @dsp = CaTissue::DisposalEventParameters.new(:specimen => specimen, :user => specimen.specimen_collection_group.receiver, :reason => 'Test')
+  end
+
+  def test_save
+    verify_save(@dsp)
+  end
+end

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

@@ -0,0 +1,38 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class LocationTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    ctr = defaults.box
+    ctr.capacity.columns = 1
+    ctr.capacity.rows = 2
+    @loc = CaTissue::Location.new(:in => ctr, :at => [0, 0])
+  end
+
+  def test_equals
+    other = CaTissue::Location.new(:in => @loc.container, :at => [@loc.column, @loc.row])
+    assert_equal(@loc, other, "Location with equal content not equal")
+  end
+
+  def test_successor
+    successor = @loc.succ
+    assert_not_nil(successor, "Successor location not created")
+    assert_not_same(@loc, successor, "Location same as successor")
+    assert_same(@loc.container, successor.container, "Location container differs from successor container")
+    assert_not_nil(successor.row, "Successor row not set")
+    assert_not_nil(successor.column, "Successor column not set")
+    assert_equal(0, successor.row, "Successor row incorrect")
+    assert_equal(1, successor.column, "Successor column incorrect")
+    assert_nil(successor.succ, "Location out of bounds")
+  end
+
+  def test_successor_bang
+    assert_same(@loc, @loc.succ!, "Location differs from successor bang")
+    assert_equal(0, @loc.column, "Successor row incorrect")
+    assert_equal(1, @loc.row, "Successor column incorrect")
+    assert_raises(IndexError, "Location out of bounds") { @loc.succ! }
+  end
+end

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

@@ -0,0 +1,62 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+
+class MetadataTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  OVERRIDE_CONFIG_FILE = 'test/fixtures/catissue/domain/conf/catissue_override.yaml'
+
+  def setup
+    super
+    @metadata = CaTissue::CollectionProtocol.metadata
+  end
+
+  def test_domain_attribute
+    assert(!@metadata.domain_attribute?(:title), 'String attribute considered domain attribute')
+    assert(@metadata.domain_attribute?(:collection_protocol_events), 'Domain collection attribute not recognized')
+  end
+
+  def test_collection_attribute
+    assert(!@metadata.collection_attribute?(:principal_investigator), 'Atomic attribute considered a collection')
+    assert(@metadata.collection_attribute?(:collection_protocol_events), 'Domain collection attribute not recognized as collection')
+  end
+
+  def test_invalid_attribute
+    assert(!@metadata.attributes.include?(:parent_collection_protocol), 'Attribute marked as invalid recognized')
+  end
+
+  def test_secondary_key
+    assert(!@metadata.secondary_key_attributes.empty?, 'Secondary key not set')
+    assert_equal([:short_title], @metadata.secondary_key_attributes.to_a, 'Secondary key incorrect')
+  end
+
+  def test_mandatory_attributes
+    assert(@metadata.mandatory_attributes.include?(:short_title), 'Secondary key not in required key')
+    assert(@metadata.mandatory_attributes.include?(:start_date), 'Required attribute not found')
+  end
+
+  # TODO - enable config override and retest.
+
+  def test_secondary_key_override
+    # save the standard properties
+    properties = CaTissue.access_properties.copy_recursive
+    # load the override properties
+    CaTissue.load_access_properties(OVERRIDE_CONFIG_FILE)
+    @metadata = CaRuby::Metadata.new(CaTissue::CollectionProtocol)
+    assert_equal([:title], @metadata.secondary_key_attributes, 'Secondary key not overridden')
+    # restore the standard properties
+    CaTissue.access_properties.keys.each { |key| CaTissue.access_properties[key] = properties[key] }
+  end
+
+  def test_mandatory_attributes_override
+    # save the standard properties
+    properties = CaTissue.access_properties.copy_recursive
+    # load the override properties
+    CaTissue.load_access_properties(OVERRIDE_CONFIG_FILE)
+    @metadata = CaRuby::Metadata.new(CaTissue::CollectionProtocol)
+    assert(@metadata.mandatory_attributes.include?(:sequence_number), 'Required attribute override not added')
+    assert(!@metadata.mandatory_attributes.include?(:start_date), 'Required attribute retained after override')
+    # restore the standard properties
+    CaTissue.access_properties.keys.each { |key| CaTissue.access_properties[key] = properties[key] }
+  end
+end

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

@@ -0,0 +1,26 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+
+class ParticipantMedicalIdentifierTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @pmi = CaTissue::ParticipantMedicalIdentifier.new
+  end
+
+  def test_i_to_s_conversion
+    @pmi.medical_record_number = 2
+    assert_equal('2', @pmi.medical_record_number, "MRN numeric argument not converted to string")
+  end
+
+  # Tests creating and fetching a participant.
+  def test_save
+    @pmi.medical_record_number = Uniquifier.qualifier
+    @pmi.site = defaults.tissue_bank
+    @pmi.participant = CaTissue::Participant.new(:name => 'Test Participant'.uniquify)
+    verify_save(@pmi)
+    # update the PMI
+    @pmi.medical_record_number = Uniquifier.qualifier
+    verify_save(@pmi)
+  end
+end

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

@@ -0,0 +1,96 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+
+class ParticipantTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @pnt = CaTissue::Participant.new(:name => 'Test Participant'.uniquify)
+  end
+
+  def test_defaults
+    verify_defaults(@pnt)
+  end
+
+  # Tests parsing the patient name.
+  def test_name
+    @pnt.name = 'John Q. Doe'
+    assert_equal('John', @pnt.first_name, 'Person first name incorrect')
+    assert_equal('Q.', @pnt.middle_name, 'Person middle name incorrect')
+    assert_equal('Doe', @pnt.last_name, 'Person last name incorrect')
+  end
+
+  # Tests the participant SSN secondary key and MRN alternate key.
+  def test_key
+    mrn = '5555'
+    pmi = @pnt.add_mrn(defaults.tissue_bank, '5555')
+    assert_equal(pmi, @pnt.key, 'Person key is not the MRN')
+    # add the preferred SSN key
+    expected = @pnt.social_security_number = '555-55-5555'
+    assert_equal(expected, @pnt.key, 'Person key is not the SSN')
+  end
+  
+  # Tests making a participant lab annotation. 
+  def test_clinical_annotation
+    labs = @pnt.lab_annotations
+    assert(labs.empty?, "Labs not empty at start")
+    lab = CaTissue::Participant::Clinical::LabAnnotation.new.merge_attributes(:lab_test_name => 'Test Lab', :participant => @pnt)
+    labs = @pnt.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")
+  end
+
+  # Tests creating and fetching a participant.
+  def test_save
+    verify_save(@pnt)
+  end
+
+  def test_save_alcohol_annotation
+    alc = CaTissue::Participant::Clinical::AlcoholHealthAnnotation.new.merge_attributes(:drinks_per_week => 4, :years_agent_free => 2, :participant => @pnt)
+    verify_save(alc)
+  end
+
+  # Tests saving a participant lab annotation. 
+  def test_save_lab_annotation
+    date = DateTime.new(2010, 10, 10)
+    lab = CaTissue::Participant::Clinical::LabAnnotation.new.merge_attributes(:other_lab_test_name => 'Test Lab', :test_date => date, :participant => @pnt)
+    verify_save(lab)
+    assert_not_nil(lab.identifier, "Lab not saved")
+  end
+  
+  def test_save_diagnosis_annotation
+    date = DateTime.new(2010, 10, 10)
+    dgn = CaTissue::Participant::Clinical::NewDiagnosisHealthAnnotation.new.merge_attributes(
+      :name_of_procedure => 'Biopsy of prostate', :date_of_examination => date, :participant => @pnt)
+    verify_save(dgn)
+  end
+  
+  def test_save_treatment_annotation
+    date = DateTime.new(2010, 10, 10)
+    trt = CaTissue::Participant::Clinical::TreatmentAnnotation.new.merge_attributes(:other_agent => 'Radical Prostatectomy', :participant => @pnt)
+    dtn = CaTissue::Participant::Clinical::Duration.new.merge_attributes(:start_date => date, :end_date => date, :duration_in_days => 1, :treatment_annotation => trt)
+    verify_save(trt)
+  end
+  
+  # caTissue alert - The RadiationTherapy DE class is not supported, since it is not a primary entity. RadRXAnnotation is used instead.
+  # 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.merge_attributes(:other_agent => 'Adjuvant Radiation Therapy', :participant => @pnt)
+    verify_save(rdx)
+  end
+  
+  def test_save_exam_annotation
+    exam = CaTissue::Participant::Clinical::HealthExaminationAnnotation.new.merge_attributes(
+      :name_of_procedure => 'Prostatectomy', :participant => @pnt)
+    verify_save(exam)
+  end
+  
+  def test_save_recurrence_exam_annotation
+    exam = CaTissue::Participant::Clinical::LocalRecurrenceHealthExaminationAnnotation.new.merge_attributes(
+      :name_of_procedure => 'Prostatectomy', :clinical_diagnosis => 'Malignant melanoma - NOS', :participant => @pnt)
+    verify_save(exam)
+  end
+end