caruby-tissue 1.3.1 → 1.3.2

data/test/fixtures/catissue/domain/conf/catissue_override.yaml

@@ -0,0 +1,9 @@
+# Tests merging attribute properites.
+
+secondary_key_attributes:
+  CollectionProtocol:
+    - title
+
+required_attributes:
+  CollectionProtocol:
+    - sequenceNumber

data/test/fixtures/catissue/extract/conf/scg_extract.yaml

@@ -0,0 +1,3 @@
+fields: test/fixtures/catissue/extract/conf/scg_fields.yaml
+output: test/results/catissue/extract/scg.csv
+target: SpecimenCollectionGroup

data/test/fixtures/catissue/extract/conf/scg_fields.yaml

@@ -0,0 +1,3 @@
+MRN: registration.participant_identifier
+SPN: surgical_pathology_number
+Collection Date: collection_event_parameters.timestamp

data/test/fixtures/catissue/extract/conf/spc_extract.yaml

@@ -0,0 +1,3 @@
+fields: test/fixtures/catissue/extract/conf/spc_fields.yaml
+output: test/results/catissue/extract/spc.csv
+target: TissueSpecimen

data/test/fixtures/catissue/extract/conf/spc_fields.yaml

@@ -0,0 +1,4 @@
+MRN: specimen_collection_group.registration.participant_identifier
+SPN: specimen_collection_group.surgical_pathology_number
+Collection Date: specimen_collection_group.collection_event_parameters.timestamp
+Quantity: initial_quantity

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

@@ -0,0 +1,202 @@
+require 'singleton'
+require 'caruby/util/uniquifier'
+require 'catissue'
+
+module CaTissueTest
+  # Error setting up the test fixture.
+  class TestError < RuntimeError; end
+
+  def self.defaults
+    Defaults.instance
+  end
+
+  # caTissue test default admin fixture.
+  class Defaults
+    include Singleton, Enumerable
+
+    attr_reader :tissue_bank, :protocol, :registration, :specimen,
+      :specimen_requirement, :specimen_collection_group, :box
+
+    def initialize
+      super
+      populate
+    end
+
+    # Retusns this fixture's domain objects.
+    def domain_objects
+      instance_variables.map { |iv| instance_eval iv }.select { |value| CaRuby::Resource === value }
+    end
+
+    # Adds default values to this fixture's domain objects.
+    def add_defaults
+      domain_objects.each { |obj| obj.add_defaults unless obj.equal?(specimen) }
+      # Add specimen default values last, since SCG add_specimens propagates the collection event
+      # necessary to set the default specimen label.
+      specimen.add_defaults
+      self
+    end
+
+    # Fetches the default instances from the database. Creates new objects if necesssary.
+    #
+    # Raises ValidationError if a domain object fails validation.
+    def validate
+      # identifiers are required for validation; these are removed following validation
+      objs_without_ids = domain_objects.select { |obj| obj.identifier.nil? }
+      objs_without_ids.each_with_index { |obj, index| obj.identifier = index + 1 }
+      domain_objects.each { |obj| obj.validate }
+      # restore null identifiers
+      objs_without_ids.each { |obj| obj.identifier = nil }
+      self
+    end
+
+    # Creates this fixture's {#domain_objects} in the database, if necessary.
+    def ensure_exists
+      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.
+    #
+    # @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
+      @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
+      self
+    end
+    
+    private
+
+    # Adds data to this fixture.
+    #
+    # @return this fixture
+    def populate
+      logger.debug { "Populating the test fixture..." }
+      # the test institution
+      inst = CaTissue::Institution.new(:name => 'Test Institution')
+
+      # the standard test address
+      addr = CaTissue::Address.new
+      addr.city = 'Test City'
+      addr.state = 'Other'
+      addr.country = 'Niue'
+      addr.zipCode = '55555'
+      addr.street = '555 Test St'
+      addr.phoneNumber = '555-555-5555'
+
+      # the test department
+      dept = CaTissue::Department.new(:name => 'Test Department')
+
+      # the test cancer center
+      cc = CaTissue::CancerResearchGroup.new(:name => 'Test Cancer Center')
+
+      # the test tissue bank coordinator
+      coord = CaTissue::User.new
+      coord.loginName = coord.emailAddress = 'test_coordinator@example.edu'
+      coord.lastName = 'Coordinator'
+      coord.firstName = 'Test'
+      coord.address = addr.copy
+      coord.institution = inst
+      coord.department = dept
+      coord.cancer_research_group = cc
+      coord.add_defaults
+
+      # the test surgeon
+      surgeon = CaTissue::User.new
+      surgeon.loginName = surgeon.emailAddress = 'test_surgeon@example.edu'
+      surgeon.lastName = 'Scientist'
+      surgeon.firstName = 'Test'
+      surgeon.address = addr.copy
+      surgeon.institution = inst
+      surgeon.department = dept
+      surgeon.cancer_research_group = cc
+
+      # the test PI
+      pi = CaTissue::User.new
+      pi.loginName = pi.emailAddress = 'test_scientist@example.edu'
+      pi.lastName = 'Scientist'
+      pi.firstName = 'Test'
+      pi.address = addr.copy
+      pi.institution = inst
+      pi.department = dept
+      pi.cancer_research_group = cc
+
+      # the test hospital
+      hospital = CaTissue::Site.new(
+        :site_type => CaTissue::Site::SiteType::COLLECTION,
+        :name => 'Test Collection Site',
+        :address => addr.copy,
+        :coordinator => coord
+      )
+
+      # the test tissue bank
+      @tissue_bank = CaTissue::Site.new(
+        :site_type => CaTissue::Site::SiteType::REPOSITORY,
+        :name => 'Test Tissue Bank',
+        :address => addr.copy,
+        :coordinator => coord
+      )
+
+      # the test participant
+      pnt = CaTissue::Participant.new(:name => 'Test Participant')
+
+      # add the participant mrn
+      mrn = 555555
+      pnt.add_mrn(hospital, mrn)
+
+      # the test collection protocol
+      @protocol = CaTissue::CollectionProtocol.new(
+        :short_title => 'Test CP',
+        :principal_investigator => pi
+      )
+
+      # the test consent tier
+      ctier = CaTissue::ConsentTier.new(:statement => 'Test Consent Statement')
+      @protocol.consent_tiers << ctier
+
+      # the collection event template
+      cpe = CaTissue::CollectionProtocolEvent.new(:protocol => @protocol)
+
+      # the participant collection registration
+      @registration = @protocol.register(pnt)
+      # add a consent tier response
+      rsp = CaTissue::ConsentTierResponse.new(:consent_tier => ctier)
+      @registration.consent_tier_responses << rsp
+
+      # the specimen requirement template
+      @specimen_requirement = CaTissue::TissueSpecimenRequirement.new(
+        :collection_event => cpe,
+        :specimen_type => 'Frozen Tissue',
+        :specimen_characteristics => CaTissue::SpecimenCharacteristics.new,
+        :pathological_status => 'Malignant')
+
+      # the sole tissue specimen
+      @specimen = CaTissue::Specimen.create_specimen(:requirement => @specimen_requirement, :initial_quantity => 4.0)
+
+      # the SCG
+      @specimen_collection_group = @protocol.add_specimens(
+        @specimen,
+        :participant => pnt,
+        :collection_event => cpe,
+        :collection_site => hospital,
+        :receiver => coord)
+
+      # a storage container
+      frz_type = CaTissue::StorageType.new(:name => 'Test Freezer', :columns => 10, :rows => 1, :row_label => 'Rack')
+      rack_type = CaTissue::StorageType.new(:name => 'Test Rack', :columns => 10, :rows => 10)
+      box_type = CaTissue::StorageType.new(:name => 'Test Box', :columns => 10, :rows => 10)
+      frz_type << rack_type
+      rack_type << box_type
+      box_type << 'Tissue'
+      # a sample freezer box
+      @box = CaTissue::StorageContainer.new(:storage_type => box_type, :site => @tissue_bank)
+
+      logger.debug { "Test fixture populated." }
+      self
+    end
+  end
+end

data/test/lib/catissue/database/controlled_values_test.rb

@@ -0,0 +1,47 @@
+$:.unshift 'lib'
+$:.unshift '../caruby/lib'
+
+require "test/unit"
+require 'caruby/util/log'
+require 'caruby/util/uniquifier'
+require 'catissue/database/controlled_values'
+
+class ControlledValuesTest < Test::Unit::TestCase
+  LOG_FILE = 'test/results/catissue/log/catissue.log'
+
+  def setup
+    CaRuby::Log.instance.open(LOG_FILE, :debug => true)
+  end
+
+# works but takes a long time
+#  def test_search_by_public_id
+#    tissue_sites = CaTissue::ControlledValues.instance.for_public_id(:tissue_site)
+#    assert_not_nil(tissue_sites, "Tissue site CVs not loaded")
+#    parent = tissue_sites.detect { |cv| cv.value == 'DIGESTIVE ORGANS' }
+#    assert_not_nil(parent, "DIGESTIVE ORGANS tissue site CVs not loaded")
+#    child = parent.children.detect { |cv| cv.value == 'ESOPHAGUS' }
+#    assert_not_nil(child, "DIGESTIVE ORGANS CV missing ESOPHAGUS child")
+#    gc = child.children.detect { |cv| cv.value == 'Esophagus, NOS' }
+#    assert_not_nil(gc, "ESOPHAGUS CV missing 'Esophagus, NOS' child")
+#    assert(!parent.children.include?(gc), "DIGESTIVE ORGANS CV children incorrectly includes ESOPHAGUS child")
+#    assert(parent.descendants.include?(gc), "DIGESTIVE ORGANS CV missing 'Esophagus, NOS' descendant")
+#  end
+
+  def test_find
+    assert_not_nil(CaTissue::ControlledValues.instance.find(:tissue_site, 'Esophagus, NOS'), "'Esophagus, NOS' CV not found")
+  end
+
+  def test_find_case_insensitive
+    assert_not_nil(CaTissue::ControlledValues.instance.find(:tissue_site, 'esophagus, NOS'), "Case-insensitive look-up inoperative")
+  end
+
+  def test_create_delete
+    cv = CaTissue::ControlledValue.new
+    cv.public_id = :tissue_site
+    cv.value = 'Test Tissue Site'.uniquify
+    assert_same(cv, CaTissue::ControlledValues.instance.create(cv), "CV not created")
+    assert_same(cv, CaTissue::ControlledValues.instance.find(cv.public_id, cv.value), "Created CV not found")
+    assert_nothing_raised("CV not deleted") { CaTissue::ControlledValues.instance.delete(cv) }
+    assert_nil(CaTissue::ControlledValues.instance.find(cv.public_id, cv.value), "Deleted CV found")
+  end
+end

data/test/lib/catissue/database/database_test.rb

@@ -0,0 +1,28 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+
+class CaTissueDatabaseTest < Test::Unit::TestCase
+  LOG_FILE = 'test/results/catissue/log/catissue.log'
+
+  def setup
+    CaRuby::Log.instance.open(LOG_FILE, :debug => true)
+    @database = CaTissue::Database.instance
+  end
+
+  def test_match_specimen
+    a = CaTissue::TissueSpecimen.new(:specimen_type => 'Fresh Tissue')
+    b = CaTissue::TissueSpecimen.new(:specimen_type => 'Fresh Tissue')
+    c1 = a.derive(:specimen_type => 'Fixed Tissue')
+    c2 = a.derive(:specimen_type => 'Fixed Tissue')
+    d = b.derive(:specimen_type => 'Fixed Tissue')
+    e1 = a.derive(:specimen_type => 'Frozen Tissue', :pathological_status => 'Normal')
+    e2 = a.derive(:specimen_type => 'Frozen Tissue', :pathological_status => 'Malignant')
+    f1 = b.derive(:specimen_type => 'Frozen Tissue', :pathological_status => 'Malignant')
+    f2 = b.derive(:specimen_type => 'Frozen Tissue', :pathological_status => 'Normal')
+    f3 = b.derive(:specimen_type => 'Frozen Tissue', :pathological_status => 'Normal')
+    actual = @database.instance_eval do
+      collect_matches([a, e1, c1, e2, c2], [f1, b, f2, d, f3])
+    end
+    expected = {a => b, c1 => d, e1 => f2, e2 => f1}
+    assert_equal(expected, actual, "Specimen match incorrect")
+  end
+end

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

@@ -0,0 +1,53 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'caruby/util/uniquifier'
+
+class AddressTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    # make the unique test address
+    @address = CaTissue::Address.new
+    @address.city = 'Test City'
+    @address.state = 'Other'
+    @address.country = 'US'
+    @address.zip_code = '55555'
+    @address.street = '555'.uniquify + ' Test St'
+    @address.phone_number = '555-555-5555'
+  end
+
+  # Tests the key method for a domain class without a secondary key.
+  def test_non_secondary_key
+    # make an address
+    @address = CaTissue::Address.new
+    @address.identifier = 1
+    expected = @address.identifier
+    assert_equal(expected, @address.key, 'Key incorrect')
+  end
+
+  def test_defaults
+    verify_defaults(@address)
+  end
+
+  def test_merge_identifier
+    from = CaTissue::User.new(:address => @address)
+    to = CaTissue::User.new(:address => @address.copy)
+    from.address.identifier = 555
+    to.merge_attributes(from)
+    assert_equal(555, to.address.identifier, "Address identifier not merged")
+  end
+
+  def test_save
+    database.create(@address)
+    assert_not_nil(@address.identifier, "Address not created")
+    @address.zip_code = '111111'
+    @address.phone_number = nil
+    database.update(@address)
+    template = @address.copy
+    template.zip_code = nil
+    fetched = database.query(template).first
+    assert_not_nil(fetched, "Address not found")
+    assert_equal('111111', fetched.zip_code, "Address zipcode not updated")
+    assert_nil(fetched.phone_number, "Address phone number not cleared by update")
+  end
+end

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

@@ -0,0 +1,25 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class BaseHaematologyPathologyTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @scg = defaults.specimen_collection_group
+    @annotation = CaTissue::PathologyScg::BaseHaematologyPathologyAnnotation.new(:specimen_collection_group => @scg)
+    @histology = CaTissue::PathologyScg::HistologicType.new(:base_pathology_annotation => @annotation, :histologic_type => 'Adenocarcinoma - NOS')
+    @finding = CaTissue::PathologyScg::AdditionalFinding.new(:base_pathology_annotation => @annotation, :pathologic_finding => 'Test finding')
+    @details = CaTissue::PathologyScg::Details.new(:additional_finding => @finding, :detail => 'Test detail')
+  end
+
+  def test_dependents
+    assert_equal([@histology], @annotation.histologic_type.to_a, "Annotation histologic types incorrect")
+    assert_equal([@finding], @annotation.additional_finding.to_a, "Annotation additional findings incorrect")
+    assert_equal([@details], @finding.details.to_a, "Finding details incorrect")
+  end
+
+  def test_save
+    verify_save(@annotation)
+  end
+end

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

@@ -0,0 +1,27 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+require 'test/fixtures/lib/catissue/defaults_test_fixture'
+
+class CaTissueTestDefaultsTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  attr_reader :defaults
+
+  def setup
+    super
+    @defaults = CaTissueTest::Defaults.instance
+  end
+
+  def test_validation
+    assert_nothing_raised(ValidationError, "Defaults validation unsuccessful") { defaults.add_defaults.validate }
+  end
+
+  # Fetches the test data, creating new objects if necessary
+  def test_find
+    assert_nothing_raised(CaRuby::DatabaseError, "Defaults store unsuccessful") { defaults.each { |obj| database.find(obj) } }
+  end
+
+  # Store the test data
+  def test_save
+    defaults.each { |obj| verify_save(obj) }
+  end
+end

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

@@ -0,0 +1,12 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+
+class CapacityTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  # Verifies the :rows and :columns aliases.
+  def test_merge_attributes
+    cpc = CaTissue::Capacity.new(:columns => 5, :rows => 5)
+    assert_equal(5, cpc.one_dimension_capacity, "Rows incorrect")
+    assert_equal(5, cpc.two_dimension_capacity, "Columns incorrect")
+  end
+end

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

@@ -0,0 +1,24 @@
+require File.join(File.dirname(__FILE__), '..', 'test_case')
+
+class CollectionEventParametersTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  attr_reader :event_params
+
+  def setup
+    super
+    scg = CaTissue::SpecimenCollectionGroup.new
+    collector = CaTissue::User.new
+    @event_params = CaTissue::SpecimenEventParameters.create_parameters(:collection, scg, :user => collector)
+  end
+
+  def test_defaults
+    event_params.add_defaults
+    assert_not_nil(event_params.timestamp, 'Timestamp not set to default')
+  end
+  
+  # Test updating an auto-created CollectionEventParameters
+  def test_create
+    
+  end
+end