caruby-tissue 1.5.6 → 2.1.1

data/test/lib/examples/galena/tissue/migration/annotation_test.rb

@@ -1,29 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class AnnotationTest < Test::Unit::TestCase
-      include MigrationTestCase
-    
-      def test_target
-        verify_target(:annotation, :target => CaTissue::SpecimenCollectionGroup) do |scg|
-          pth = scg.pathology.first
-          assert_not_nil(pth, "Missing #{scg} pathology annotation proxy")
-          pst = pth.radical_prostatectomy_pathology_annotations.first
-          assert_not_nil(pst, "Missing #{scg} prostate annotation")
-          assert_not_nil(pst.comment, "Missing #{pst} comments")
-          gls = pst.gleason_score
-          assert_not_nil(pst, "Missing #{pst} gleason score")
-          assert_equal('3', gls.primary_pattern_score, "Gleason score incorrect")
-          grd = pst.histologic_grades.first
-          assert_not_nil(grd, "Missing #{pst} grade")
-          assert_equal('2', grd.grade, "Grade incorrect")
-        end
-      end
-    
-      def test_save
-        verify_save(:annotation, :target => CaTissue::SpecimenCollectionGroup)
-      end
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/filter_test.rb

@@ -1,29 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class FilterMigrationTest < Test::Unit::TestCase
-      include Galena::Tissue::MigrationTestCase
-    
-      def test_filter
-        verify_target(:filter, :bad => BAD_FILE) do |spc|
-          assert_not_nil(spc.initial_quantity, "Missing quantity")
-          scg = spc.specimen_collection_group
-          assert_not_nil(scg, "Missing SCG")
-          pnt = scg.registration.participant
-          assert_not_nil(pnt, "Missing Participant")
-          assert_not_nil(pnt.first_name, "Missing first name")
-          assert_not_nil(pnt.last_name, "Missing last name")
-        end
-      end
-    
-      def test_save
-        verify_save(:filter, :bad => BAD_FILE)
-      end
-      
-      private
-      
-      BAD_FILE = 'test/results/examples/galena/bad.csv'
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/frozen_test.rb

@@ -1,36 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-require 'galena/tissue/seed/defaults'
-
-module Galena
-  module Tissue
-    class FrozenMigrationTest < Test::Unit::TestCase
-      include MigrationTestCase
-      
-      # Makes the {Galena::Defaults#freezer_type} container type hierarchy, if necessary.
-      def setup
-        super
-        defaults.freezer_type.find(:create)
-      end
-
-      def test_target
-        verify_target(:frozen) do |spc|
-          assert_equal('Frozen Tissue', spc.specimen_type, "#{spc} type incorrect")
-          pos = spc.position
-          assert_not_nil(pos, "#{spc} missing position")
-          assert_not_nil(pos.holder, "#{pos} missing storage container")
-          assert_same(spc, pos.occupant,"#{pos} occupant incorrect")
-        end
-      end
-
-      def test_save
-        # rename the target box
-        box = CaTissue::StorageContainer.new(:name => 'Galena Box 7')
-        if box.find then
-          box.name = box.name.uniquify
-          box.save
-        end
-        verify_save(:frozen)
-      end
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/general_test.rb

@@ -1,56 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class GeneralMigrationTest < Test::Unit::TestCase
-      include Galena::Tissue::MigrationTestCase
-    
-      def test_target
-        verify_target(:general) do |spc|
-          assert_not_nil(spc.initial_quantity, "Missing quantity")
-          scg = spc.specimen_collection_group
-          assert_not_nil(scg, "Missing SCG")
-          pnt = scg.registration.participant
-          assert_not_nil(pnt, "Missing Participant")
-          pmi = pnt.participant_medical_identifiers.first
-          assert_not_nil(pmi, "Missing PMI")
-          mrn = pmi.medical_record_number
-          assert_not_nil(mrn, "Missing MRN")
-          rep = scg.received_event_parameters
-          assert_not_nil(rep, "Missing REP")
-          assert_not_nil(rep.timestamp, "Missing received date")
-        end
-      end
-      
-      def test_save
-        # Clear a space for the specimen
-        box = CaTissue::StorageContainer.new(:name => 'Galena Box 1')
-        if box.find then
-          box.name = box.name.uniquify
-          box.save
-        end
-        
-        # Make the surgeon user, if necessary, by copying the required attributes from the coordinator.
-        crd = defaults.tissue_bank.coordinator
-        srg = defaults.tissue_bank.coordinator.copy(:cancer_research_group, :department, :institution)
-        srg.address = crd.address.copy
-        srg.email_address = 'serge.on@galena.edu'
-        srg.first_name = 'Serge'
-        srg.last_name = 'On'
-        srg.find(:create)
-    
-        # migrate the Specimen input record
-        verify_save(:general) do |spc|
-          logger.debug { "Verifying saved #{spc}..." }
-          assert_equal('Frozen Tissue', spc.specimen_type, "#{spc} specimen type incorrect")
-          scg = spc.specimen_collection_group
-          assert_not_nil(scg, "#{spc} missing SCG")
-          assert_equal('Complete', scg.collection_status, "#{scg} collection status incorrect")
-          spcs = scg.specimens
-          assert_equal(1, spcs.size, "#{scg} specimen count incorrect")
-          assert_same(spc, spcs.first, "#{scg} specimen incorrect")
-       end
-     end
-   end
-  end
-end

data/test/lib/examples/galena/tissue/migration/participant_test.rb

@@ -1,61 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class ParticipantMigrationTest < Test::Unit::TestCase
-      include MigrationTestCase
-    
-      def test_target
-        verify_target(:participant, :target => CaTissue::Participant)
-      end
-    
-      def test_save
-        clear
-        # test the create
-        verify_save(:participant, :target => CaTissue::Participant)
-      end
-      
-      def test_create
-        clear
-        # make the test participant
-        pnt = CaTissue::Participant.new(:social_security_number => '333-66-9999')
-        pnt.create
-        migrate_to_database(:participant, :target => CaTissue::Participant, :create=>true)
-        # Verify that the name was not updated.
-        pnt.identifier = nil
-        pnt.find
-        assert_nil(pnt.last_name, "Existing participant was updated despite the migration :create flag")
-      end
-      
-      def test_create_with_alternate_id
-        clear
-        # make the test participant
-        pnt = CaTissue::Participant.new(:first_name => 'Rufus', :last_name => 'Firefly')
-        # move aside duplicates
-        pnt.query.each do |dup|
-          dup.last_name = dup.last_name.uniquify
-          dup.save
-        end
-        pnt.create
-        migrate_to_database(:participant, :target => CaTissue::Participant, :shims => [ALT_ID_SHIM], :create=>true)
-        # Verify that the SSN was not updated.
-        pnt.identifier = nil
-        pnt.find
-        assert_nil(pnt.social_security_number, "Existing participant with alternate key was updated despite the migration :create flag")
-      end
-      
-      private
-      
-      ALT_ID_SHIM = 'test/fixtures/lib/examples/galena/migration/alt_key_shims.rb'
-      
-      def clear
-        # push aside the existing test participant
-        pnt = CaTissue::Participant.new(:social_security_number => '333-66-9999')
-        if pnt.find then
-          pnt.social_security_number = nil
-          pnt.update
-        end
-      end
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/registration_test.rb

@@ -1,17 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class RegistrationTest < Test::Unit::TestCase
-      include MigrationTestCase
-    
-      def test_target
-        verify_target(:registration, :target => CaTissue::SpecimenCollectionGroup)
-      end
-    
-      def test_save
-        verify_save(:registration, :target => CaTissue::SpecimenCollectionGroup)
-      end
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/seedify.rb

@@ -1,119 +0,0 @@
-require 'caruby/util/inflector'
-require 'caruby/migration/migratable'
-require 'galena/tissue/seed/defaults'
-
-module CaTissue
-  # Augment the classes below with sufficient content to pass the create mandatory attribute validation.
-  #  This simulates an existing administrative object for testing purposes.
-  shims CollectionProtocol, CollectionProtocolEvent, Site, StorageContainer, User
-  
-  class CollectionProtocol
-    # Augments {CaRuby::Migratable#migrate} for the Galena example by adding the following defaults:
-    # * the CP principal_investigator defaults to the {Galena::Seed::Defaults#protocol} PI
-    # * if the sites is empty, then the {Galena::Seed::Defaults#tissue_bank} is added
-    #   to the CP sites
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      self.title ||= migration_default_title(migrated)
-      self.principal_investigator ||= Galena::Seed.defaults.protocol.principal_investigator
-      sites << Galena::Seed.defaults.tissue_bank if sites.empty?
-      coordinators << Galena::Seed.defaults.tissue_bank.coordinator if coordinators.empty?
-    end
-    
-    private
-    
-    # @param (see #migrate)
-    # @return [String, nil] the short title of the {Galena::Seed::Defaults} protocol which
-    #   matches this protocol's event, or nil if no match 
-    def migration_default_title(migrated)
-      cpe = migrated.detect { |obj| CaTissue::CollectionProtocolEvent === obj } || return
-      pcl = Galena::Seed.defaults.protocols.detect { |p| p.events.first.label == cpe.label } || return
-      pcl.title
-    end
-  end
-  
-  class CollectionProtocolEvent
-    # Augments {CaRuby::Migratable#migrate} for the example by adding the following defaults:
-    # * create a {CaTissue::TissueSpecimenRequirement}
-    # * copy the event point from the matching {Galena::Seed::Defaults} CPE, if any
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      match = Galena::Seed.defaults.protocols.detect_value do |pcl|
-        cpe = pcl.events.first
-        cpe if cpe.label == label
-      end
-      if match then
-        self.event_point ||= match.event_point
-        rqmt = match.requirements.first
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => self, :specimen_type => rqmt.specimen_type)
-      else
-        CaTissue::TissueSpecimenRequirement.new(:collection_event => self)
-      end
-    end
-  end
-
-  class Site
-    # Augments {CaRuby::Migratable#migrate} for the example by merging the content of the
-    # {Galena::Seed::Defaults} site which matches on this Site's name, if any.
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      # Match the site by name. Account for uniquification by a partial match, e.g.
-      # 'Galena_Hospital_41893443' matches the site named 'Galena Hospital'.
-      tmpl = TEMPLATES.detect { |site| name[site.name.gsub('_', ' ')] }
-      # merge the default mandatory attribute values
-      if tmpl then merge(tmpl, mandatory_attributes) end
-    end
-    
-    private
-    
-    TEMPLATES = [Galena::Seed.defaults.hospital, Galena::Seed.defaults.tissue_bank]
-  end
-
-  class StorageContainer
-    # Augments {CaRuby::Migratable#migrate} for the example by setting the
-    # the container site and type to the {Galena::Seed::Defaults}
-    # box site and type, resp.
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      self.site ||= Galena::Seed.defaults.tissue_bank
-      self.storage_type ||= Galena::Seed.defaults.box_type
-    end
-  end
-  
-  class User
-    # Augments {CaRuby::Migratable#migrate} for the example as follows:
-    # * infer the first and last name from the email address
-    # * copy the address and organizations from the tissue bank coordinator 
-    #
-    # @param (see CaRuby::Migratable#migrate)
-    def migrate(row, migrated)
-      super
-      # invent the mandatory name fields based on the email address, if necessary
-      if email_address then
-        n1, n2 = email_address[/[^@]+/].split('.')
-        if n2 then
-          first, last = n1, n2
-        else
-          first = 'Oscar'
-          last = n1.capitalize
-        end
-        self.first_name = n1.capitalize
-        self.last_name = n2.capitalize
-      end
-      # the coordinator serves as the User content template
-      coord = Galena::Seed.defaults.hospital.coordinator
-      # deep copy of the address
-      self.address = coord.address.copy
-      # shallow copy of the mandatory references
-      merge(coord, [:cancer_research_group, :department, :institution])
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/simple_test.rb

@@ -1,30 +0,0 @@
-require File.join(File.dirname(__FILE__), 'test_case')
-
-module Galena
-  module Tissue
-    class SimpleTest < Test::Unit::TestCase
-      include MigrationTestCase
-    
-      def test_target
-        verify_target(:simple) do |spc|
-          assert_not_nil(spc.initial_quantity, "Missing quantity")
-          scg = spc.specimen_collection_group
-          assert_not_nil(scg, "Missing SCG")
-          pnt = scg.registration.participant
-          assert_not_nil(pnt, "Missing Participant")
-          pmi = pnt.participant_medical_identifiers.first
-          assert_not_nil(pmi, "Missing PMI")
-          mrn = pmi.medical_record_number
-          assert_not_nil(mrn, "Missing MRN")
-          rep = spc.received_event_parameters
-          assert_not_nil(rep, "Missing REP")
-          assert_not_nil(rep.timestamp, "Missing received date")
-        end
-      end
-    
-      def test_save
-        verify_save(:simple)
-      end
-    end
-  end
-end

data/test/lib/examples/galena/tissue/migration/test_case.rb

@@ -1,72 +0,0 @@
-$:.unshift 'examples/galena/lib'
-
-require 'test/lib/catissue/migration/test_case'
-require 'galena/tissue/seed/defaults'
-
-# Inject migrate methods that simulate administrative setup.
-require File.join(File.dirname(__FILE__), 'seedify')
-
-module Galena
-  module Tissue
-    # Tests the Galena example migration.
-    module MigrationTestCase
-      include CaTissue::MigrationTestCase
-    
-      # The default migration input data directory.
-      FIXTURES = 'examples/galena/data'
-    
-      # The default migration shims directory.
-      SHIMS = 'examples/galena/lib/galena/tissue/migration'
-      
-      # The dfault migration configuration directory.
-      CONFIGS = 'examples/galena/conf/migration'
-    
-      # The migration options are obtained from the file named _fixture_+_migration.yaml+
-      # in the {CONFIGS} directory.
-      #
-      # @param [String, nil] the fixtures directory (default {FIXTURES})
-      def setup(fixtures=FIXTURES)
-        super(fixtures)
-      end
-      
-      private
-      
-      # @return [Galena::Seed::Defaults] the {Galena::Seed.defaults}
-      def defaults
-        @defaults ||= Galena::Seed.defaults
-      end
-      
-      # Adds the +:target+, +:mapping+ and +:shims+ to the options and delegates
-      # to the superclass.
-      #
-      # @see {CaTissue::MigrationTestCase#create_migrator}
-      def create_migrator(fixture, opts={})
-        opts[:target] ||= CaTissue::TissueSpecimen
-        opts[:mapping] ||= File.join(CONFIGS, "#{fixture}_fields.yaml")
-        unless opts.has_key?(:defaults) then
-          f = File.join(CONFIGS, "#{fixture}_defaults.yaml")
-          if File.exists?(f) then opts[:defaults] = f end
-        end
-        unless opts.has_key?(:filters) then
-          f = File.join(CONFIGS, "#{fixture}_values.yaml")
-          if File.exists?(f) then opts[:filters] = f end
-        end
-        unless opts.has_key?(:shims) then
-          f = File.join(SHIMS, "#{fixture}_shims.rb")
-          if File.exists?(f) then
-            opts[:shims] = [f]
-          end    
-        end
-        mgtr = super
-        if opts[:unique] then
-          defaults.protocols.each do |pcl|
-            pcl.uniquify
-            pcl.events.each { |cpe| cpe.uniquify }
-          end
-        end
-        mgtr
-      end
-    end
-  end
-end
-