caruby-tissue 1.3.1 → 1.3.2

data/test/lib/examples/galena/domain/examples_test.rb

@@ -0,0 +1,70 @@
+$:.unshift 'examples/galena/lib'
+
+require 'test/lib/catissue/test_case'
+require 'galena/seed/defaults'
+
+# Verifies the Galena caTissue usage examples.
+class ExamplesTest < Test::Unit::TestCase
+  include CaTissue::TestCase
+
+  def setup
+    super
+    @pcl = defaults.protocol
+    @pcl.title = @pcl.short_title = 'Galena CP'.uniquify
+    @pnt = CaTissue::Participant.new(:name => 'Test Participant'.uniquify)
+    @pnt.add_mrn(defaults.hospital, Uniquifier.qualifier)
+    tissue = CaTissue::Specimen.create_specimen(:class => :tissue, :type => 'Frozen Tissue', :quantity => 1.0)
+    blood = CaTissue::Specimen.create_specimen(:class => :fluid, :type => 'Whole Blood', :quantity => 10)
+    rcvr = defaults.tissue_bank.coordinator
+    @scg = @pcl.add_specimens(blood, tissue, :participant => @pnt, :receiver => rcvr)
+  end
+    
+  def defaults
+    @defaults ||= Galena::Seed.defaults.uniquify
+  end
+
+# TODO - uncomment, test and fix
+#  # Verifies the consent withdrawal usage example.
+#  def test_withdraw_consent
+#    # add a protocol consent tier
+#    @pcl.consent_tiers << ct = CaTissue::ConsentTier.new(:statement => 'Test Consent'.uniquify)
+#    # add a CPR consent tier response
+#    @scg.registration.consent_tier_responses << CaTissue::ConsentTierResponse.new(:consent_tier => ct)
+#    # create the SCG
+#    @scg.create
+#    logger.debug { "Verifying #{@scg} fluid specimen consent withdrawal..." }
+#    # the participant MRN
+#    mrn = @pnt.medical_record_number
+#    # the template to fetch a PMI for the MRN
+#    pmi = CaTissue::ParticipantMedicalIdentifier.new(:medical_record_number => mrn)
+#    # the Specimens for the individual with the MRN
+#    spcs = pmi.query(:participant, :registrations, :specimen_collection_groups, :specimens).select { |spc| spc.specimen_class == 'Fluid' }
+#    # withdraw consent and update each fetched specimen
+#    spcs.each do |spc|
+#      spc.withdraw_consent(ct)
+#      verify_save(spc)
+#    end
+#  end
+
+  # Verifies the Specimen relabel usage example.
+  def test_cp_specimens_relabel
+    @scg.create
+    @pcl.find.specimens.each do |spc|
+      spc.label = 'CP-' + spc.label
+      verify_save(spc)
+    end
+  end
+
+  # Verifies the Specimen relabel usage example.
+  def test_site_specimens_relabel
+    tb = defaults.tissue_bank
+    tb.name = tb_name = tb.name.uniquify
+    @scg.create
+    CaTissue::SpecimenCollectionGroup.new(:site => tb).query(:specimen_collection_group, :specimens).each do |spc|
+      spc.label = 'CP-' + spc.label
+      verify_save(spc)
+    end
+    # reset the default
+    tb.name = tb_name
+  end
+end

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

@@ -0,0 +1,26 @@
+require File.join(File.dirname(__FILE__), 'test_case')
+
+# Tests the Galena example migration.
+class FilterMigrationTest < Test::Unit::TestCase
+  include Galena::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

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

@@ -0,0 +1,28 @@
+require File.join(File.dirname(__FILE__), 'test_case')
+require 'galena/seed/defaults'
+
+# Tests the Galena example migration.
+module Galena
+  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|
+        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
+      verify_save(:frozen)
+    end
+  end
+end

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

@@ -0,0 +1,44 @@
+require File.join(File.dirname(__FILE__), 'test_case')
+
+# Tests the Galena example migration.
+class GeneralMigrationTest < Test::Unit::TestCase
+  include Galena::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
+    # Make the surgeon user, if necessary, by copying the required attributes from the coordinator.
+    srg = defaults.tissue_bank.coordinator.copy(:address, :cancer_research_group, :department, :institution)
+    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

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

@@ -0,0 +1,29 @@
+require File.join(File.dirname(__FILE__), 'test_case')
+
+# Tests the Galena example migration.
+module Galena
+  class SimpleMigrationTest < 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 = scg.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

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

@@ -0,0 +1,52 @@
+$:.unshift 'examples/galena/lib'
+
+require 'test/lib/catissue/migration/test_case'
+require 'galena/seed/defaults'
+
+# Inject migrate methods that simulate administrative setup.
+require File.join(File.dirname(__FILE__), 'uniquify')
+
+module Galena
+  # Tests the Galena example migration.
+  module MigrationTestCase
+    include CaTissue::MigrationTestCase
+  
+    # The migration input data directory.
+    FIXTURES = 'examples/galena/data'
+  
+    # The migration input data directory.
+    SHIMS = 'examples/galena/lib/galena/migration'
+    
+    # The migration configuration directory.
+    CONFIGS = 'examples/galena/conf/migration'
+  
+    # The migration options are obtained from the file named _fixture_+_migration.yaml+
+    # in the {CONFIGS} directory.
+    def setup
+      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")
+      shims = File.join(SHIMS, "#{fixture}_shims.rb")
+      if File.exists?(shims) then
+        sopt = opts[:shims] ||= []
+        sopt << shims
+      end
+      super
+    end
+  end
+end
+

data/test/lib/examples/galena/migration/uniquify.rb

@@ -0,0 +1,93 @@
+require 'caruby/util/inflector'
+require 'caruby/migration/migratable'
+require 'galena/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, SpecimenPosition, 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.principal_investigator ||= Galena::Seed.defaults.protocol.principal_investigator
+      sites << Galena::Seed.defaults.tissue_bank if sites.empty?
+    end
+  end
+  
+  class CollectionProtocolEvent
+    # Augments {CaRuby::Migratable#migrate} for the example by adding the following defaults:
+    # * create a {CaTissue::TissueSpecimenRequirement}
+    #
+    # @param (see CaRuby::Migratable#migrate)
+    def migrate(row, migrated)
+      super
+      CaTissue::TissueSpecimenRequirement.new(:collection_event => self)
+    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
+      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

metadata

@@ -1,200 +1,239 @@
 --- !ruby/object:Gem::Specification 
+name: caruby-tissue
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 1.3.2
+platform: ruby
+authors: 
+  - OHSU
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-11-30 00:00:00 -08:00
+default_executable: 
+dependencies: 
+  - !ruby/object:Gem::Dependency 
+    name: caruby-core
+    prerelease: false
+    requirement: &id001 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: "0"
+    type: :runtime
+    version_requirements: *id001
+description: "    The caruby-tissue gem applies the caRuby facade to the caTissue application.\n"
+email: caruby.org@gmail.com
+executables: 
+  - crtdump
+  - crtexample
+  - crtextract
+  - crtmigrate
+  - crtsmoke
 extensions: []
 
+extra_rdoc_files: []
+
+files: 
+  - bin/crtdump
+  - bin/crtexample
+  - bin/crtextract
+  - bin/crtmigrate
+  - bin/crtsmoke
+  - conf/extract/simple_fields.yaml
+  - conf/migration/filter_fields.yaml
+  - conf/migration/filter_migration.yaml
+  - conf/migration/frozen_fields.yaml
+  - conf/migration/frozen_migration.yaml
+  - conf/migration/general_fields.yaml
+  - conf/migration/general_migration.yaml
+  - conf/migration/simple_fields.yaml
+  - conf/migration/simple_migration.yaml
+  - conf/migration/small_fields.yaml
+  - conf/migration/small_migration.yaml
+  - examples/galena/README.md
+  - examples/galena/bin/seed
+  - examples/galena/conf/extract/simple_fields.yaml
+  - examples/galena/conf/migration/filter_fields.yaml
+  - examples/galena/conf/migration/frozen_fields.yaml
+  - examples/galena/conf/migration/general_fields.yaml
+  - examples/galena/conf/migration/simple_fields.yaml
+  - examples/galena/data/filter.csv
+  - examples/galena/data/frozen.csv
+  - examples/galena/data/general.csv
+  - examples/galena/data/minimal.csv
+  - examples/galena/data/simple.csv
+  - examples/galena/data/small.csv
+  - examples/galena/lib/galena.rb
+  - examples/galena/lib/galena/cli/seed.rb
+  - examples/galena/lib/galena/migration/filter_shims.rb
+  - examples/galena/lib/galena/migration/frozen_shims.rb
+  - examples/galena/lib/galena/seed/defaults.rb
+  - lib/catissue.rb
+  - lib/catissue/database.rb
+  - lib/catissue/resource.rb
+  - lib/catissue/version.rb
+  - lib/catissue/annotation/annotatable.rb
+  - lib/catissue/annotation/annotatable_class.rb
+  - lib/catissue/annotation/annotation.rb
+  - lib/catissue/annotation/annotation_class.rb
+  - lib/catissue/annotation/annotation_module.rb
+  - lib/catissue/annotation/proxy.rb
+  - lib/catissue/annotation/proxy_class.rb
+  - lib/catissue/cli/command.rb
+  - lib/catissue/cli/example.rb
+  - lib/catissue/cli/migrate.rb
+  - lib/catissue/cli/smoke.rb
+  - lib/catissue/database/controlled_value_finder.rb
+  - lib/catissue/database/controlled_values.rb
+  - lib/catissue/database/annotation/annotation_service.rb
+  - lib/catissue/database/annotation/annotator.rb
+  - lib/catissue/database/annotation/entity_facade.rb
+  - lib/catissue/database/annotation/id_generator.rb
+  - lib/catissue/database/annotation/integration_service.rb
+  - lib/catissue/database/annotation/reference_writer.rb
+  - lib/catissue/domain/abstract_domain_object.rb
+  - lib/catissue/domain/abstract_position.rb
+  - lib/catissue/domain/abstract_specimen.rb
+  - lib/catissue/domain/abstract_specimen_collection_group.rb
+  - lib/catissue/domain/address.rb
+  - lib/catissue/domain/cancer_research_group.rb
+  - lib/catissue/domain/capacity.rb
+  - lib/catissue/domain/check_in_check_out_event_parameter.rb
+  - lib/catissue/domain/collection_event_parameters.rb
+  - lib/catissue/domain/collection_protocol.rb
+  - lib/catissue/domain/collection_protocol_event.rb
+  - lib/catissue/domain/collection_protocol_registration.rb
+  - lib/catissue/domain/consent_tier_response.rb
+  - lib/catissue/domain/consent_tier_status.rb
+  - lib/catissue/domain/container.rb
+  - lib/catissue/domain/container_position.rb
+  - lib/catissue/domain/container_type.rb
+  - lib/catissue/domain/department.rb
+  - lib/catissue/domain/disposal_event_parameters.rb
+  - lib/catissue/domain/embedded_event_parameters.rb
+  - lib/catissue/domain/external_identifier.rb
+  - lib/catissue/domain/frozen_event_parameters.rb
+  - lib/catissue/domain/institution.rb
+  - lib/catissue/domain/new_specimen_array_order_item.rb
+  - lib/catissue/domain/order_details.rb
+  - lib/catissue/domain/participant.rb
+  - lib/catissue/domain/participant_medical_identifier.rb
+  - lib/catissue/domain/password.rb
+  - lib/catissue/domain/race.rb
+  - lib/catissue/domain/received_event_parameters.rb
+  - lib/catissue/domain/scg_event_parameters.rb
+  - lib/catissue/domain/site.rb
+  - lib/catissue/domain/specimen.rb
+  - lib/catissue/domain/specimen_array.rb
+  - lib/catissue/domain/specimen_array_content.rb
+  - lib/catissue/domain/specimen_array_type.rb
+  - lib/catissue/domain/specimen_characteristics.rb
+  - lib/catissue/domain/specimen_collection_group.rb
+  - lib/catissue/domain/specimen_event_parameters.rb
+  - lib/catissue/domain/specimen_position.rb
+  - lib/catissue/domain/specimen_protocol.rb
+  - lib/catissue/domain/specimen_requirement.rb
+  - lib/catissue/domain/storage_container.rb
+  - lib/catissue/domain/storage_type.rb
+  - lib/catissue/domain/transfer_event_parameters.rb
+  - lib/catissue/domain/uniquify.rb
+  - lib/catissue/domain/user.rb
+  - lib/catissue/extract/command.rb
+  - lib/catissue/extract/delta.rb
+  - lib/catissue/extract/extractor.rb
+  - lib/catissue/migration/migrator.rb
+  - lib/catissue/migration/shims.rb
+  - lib/catissue/migration/uniquify.rb
+  - lib/catissue/util/controlled_value.rb
+  - lib/catissue/util/location.rb
+  - lib/catissue/util/log.rb
+  - lib/catissue/util/person.rb
+  - lib/catissue/util/position.rb
+  - lib/catissue/util/storable.rb
+  - lib/catissue/util/storage_type_holder.rb
+  - test/fixtures/catissue/domain/conf/catissue_override.yaml
+  - test/fixtures/catissue/extract/conf/scg_extract.yaml
+  - test/fixtures/catissue/extract/conf/scg_fields.yaml
+  - test/fixtures/catissue/extract/conf/spc_extract.yaml
+  - test/fixtures/catissue/extract/conf/spc_fields.yaml
+  - test/fixtures/lib/catissue/defaults_test_fixture.rb
+  - test/lib/catissue/test_case.rb
+  - test/lib/catissue/database/controlled_values_test.rb
+  - test/lib/catissue/database/database_test.rb
+  - test/lib/catissue/domain/address_test.rb
+  - test/lib/catissue/domain/base_haemotology_pathology_test.rb
+  - test/lib/catissue/domain/ca_tissue_test_defaults_test.rb
+  - test/lib/catissue/domain/capacity_test.rb
+  - test/lib/catissue/domain/collection_event_parameters_test.rb
+  - test/lib/catissue/domain/collection_protocol_event_test.rb
+  - test/lib/catissue/domain/collection_protocol_registration_test.rb
+  - test/lib/catissue/domain/collection_protocol_test.rb
+  - test/lib/catissue/domain/container_position_test.rb
+  - test/lib/catissue/domain/department_test.rb
+  - test/lib/catissue/domain/disposal_event_parameters_test.rb
+  - test/lib/catissue/domain/location_test.rb
+  - test/lib/catissue/domain/metadata_test.rb
+  - test/lib/catissue/domain/participant_medical_identifier_test.rb
+  - test/lib/catissue/domain/participant_test.rb
+  - test/lib/catissue/domain/site_test.rb
+  - test/lib/catissue/domain/specimen_array_test.rb
+  - test/lib/catissue/domain/specimen_array_type_test.rb
+  - test/lib/catissue/domain/specimen_characteristics_test.rb
+  - test/lib/catissue/domain/specimen_collection_group_test.rb
+  - test/lib/catissue/domain/specimen_event_parameters_test.rb
+  - test/lib/catissue/domain/specimen_position_test.rb
+  - test/lib/catissue/domain/specimen_requirement_test.rb
+  - test/lib/catissue/domain/specimen_test.rb
+  - test/lib/catissue/domain/storage_container_test.rb
+  - test/lib/catissue/domain/storage_type_test.rb
+  - test/lib/catissue/domain/transfer_event_parameters_test.rb
+  - test/lib/catissue/domain/user_test.rb
+  - test/lib/catissue/extract/delta_test.rb
+  - test/lib/catissue/extract/extractor_test.rb
+  - test/lib/catissue/import/importable_module_test.rb
+  - test/lib/catissue/migration/test_case.rb
+  - test/lib/examples/galena/domain/examples_test.rb
+  - test/lib/examples/galena/migration/catissue.log
+  - test/lib/examples/galena/migration/filter_test.rb
+  - test/lib/examples/galena/migration/frozen_test.rb
+  - test/lib/examples/galena/migration/general_test.rb
+  - test/lib/examples/galena/migration/simple_test.rb
+  - test/lib/examples/galena/migration/test_case.rb
+  - test/lib/examples/galena/migration/uniquify.rb
+  - History.txt
+  - LEGAL
+  - LICENSE
+  - README.md
+has_rdoc: true
 homepage: http://rubyforge.org/projects/caruby/tissue
-executables: 
-- crtdump
-- crtexample
-- crtextract
-- crtmigrate
-- crtsmoke
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  version: 1.3.1
-  segments: 
-  - 1
-  - 3
-  - 1
+licenses: 
+  - MIT
 post_install_message: 
-date: 2010-11-30 08:00:00 +00:00
-files: 
-- bin/crtdump
-- bin/crtexample
-- bin/crtextract
-- bin/crtmigrate
-- bin/crtsmoke
-- conf/extract/simple_fields.yaml
-- conf/migration/filter_fields.yaml
-- conf/migration/filter_migration.yaml
-- conf/migration/frozen_fields.yaml
-- conf/migration/frozen_migration.yaml
-- conf/migration/general_fields.yaml
-- conf/migration/general_migration.yaml
-- conf/migration/simple_fields.yaml
-- conf/migration/simple_migration.yaml
-- conf/migration/small_fields.yaml
-- conf/migration/small_migration.yaml
-- examples/galena/README.md
-- examples/galena/bin/seed
-- examples/galena/conf/extract/simple_fields.yaml
-- examples/galena/conf/migration/filter_fields.yaml
-- examples/galena/conf/migration/frozen_fields.yaml
-- examples/galena/conf/migration/general_fields.yaml
-- examples/galena/conf/migration/simple_fields.yaml
-- examples/galena/data/filter.csv
-- examples/galena/data/frozen.csv
-- examples/galena/data/general.csv
-- examples/galena/data/minimal.csv
-- examples/galena/data/simple.csv
-- examples/galena/data/small.csv
-- examples/galena/lib/galena.rb
-- examples/galena/lib/galena/cli/seed.rb
-- examples/galena/lib/galena/migration/filter_shims.rb
-- examples/galena/lib/galena/migration/frozen_shims.rb
-- examples/galena/lib/galena/seed/defaults.rb
-- lib/catissue.rb
-- lib/catissue/database.rb
-- lib/catissue/resource.rb
-- lib/catissue/version.rb
-- lib/catissue/annotation/annotatable.rb
-- lib/catissue/annotation/annotatable_class.rb
-- lib/catissue/annotation/annotation.rb
-- lib/catissue/annotation/annotation_class.rb
-- lib/catissue/annotation/annotation_module.rb
-- lib/catissue/annotation/proxy.rb
-- lib/catissue/annotation/proxy_class.rb
-- lib/catissue/cli/command.rb
-- lib/catissue/cli/example.rb
-- lib/catissue/cli/migrate.rb
-- lib/catissue/cli/smoke.rb
-- lib/catissue/database/controlled_value_finder.rb
-- lib/catissue/database/controlled_values.rb
-- lib/catissue/database/annotation/annotation_service.rb
-- lib/catissue/database/annotation/annotator.rb
-- lib/catissue/database/annotation/entity_facade.rb
-- lib/catissue/database/annotation/id_generator.rb
-- lib/catissue/database/annotation/integration_service.rb
-- lib/catissue/database/annotation/reference_writer.rb
-- lib/catissue/domain/abstract_domain_object.rb
-- lib/catissue/domain/abstract_position.rb
-- lib/catissue/domain/abstract_specimen.rb
-- lib/catissue/domain/abstract_specimen_collection_group.rb
-- lib/catissue/domain/address.rb
-- lib/catissue/domain/cancer_research_group.rb
-- lib/catissue/domain/capacity.rb
-- lib/catissue/domain/check_in_check_out_event_parameter.rb
-- lib/catissue/domain/collection_event_parameters.rb
-- lib/catissue/domain/collection_protocol.rb
-- lib/catissue/domain/collection_protocol_event.rb
-- lib/catissue/domain/collection_protocol_registration.rb
-- lib/catissue/domain/consent_tier_response.rb
-- lib/catissue/domain/consent_tier_status.rb
-- lib/catissue/domain/container.rb
-- lib/catissue/domain/container_position.rb
-- lib/catissue/domain/container_type.rb
-- lib/catissue/domain/department.rb
-- lib/catissue/domain/disposal_event_parameters.rb
-- lib/catissue/domain/embedded_event_parameters.rb
-- lib/catissue/domain/external_identifier.rb
-- lib/catissue/domain/frozen_event_parameters.rb
-- lib/catissue/domain/institution.rb
-- lib/catissue/domain/new_specimen_array_order_item.rb
-- lib/catissue/domain/order_details.rb
-- lib/catissue/domain/participant.rb
-- lib/catissue/domain/participant_medical_identifier.rb
-- lib/catissue/domain/password.rb
-- lib/catissue/domain/race.rb
-- lib/catissue/domain/received_event_parameters.rb
-- lib/catissue/domain/scg_event_parameters.rb
-- lib/catissue/domain/site.rb
-- lib/catissue/domain/specimen.rb
-- lib/catissue/domain/specimen_array.rb
-- lib/catissue/domain/specimen_array_content.rb
-- lib/catissue/domain/specimen_array_type.rb
-- lib/catissue/domain/specimen_characteristics.rb
-- lib/catissue/domain/specimen_collection_group.rb
-- lib/catissue/domain/specimen_event_parameters.rb
-- lib/catissue/domain/specimen_position.rb
-- lib/catissue/domain/specimen_protocol.rb
-- lib/catissue/domain/specimen_requirement.rb
-- lib/catissue/domain/storage_container.rb
-- lib/catissue/domain/storage_type.rb
-- lib/catissue/domain/transfer_event_parameters.rb
-- lib/catissue/domain/user.rb
-- lib/catissue/extract/command.rb
-- lib/catissue/extract/delta.rb
-- lib/catissue/extract/extractor.rb
-- lib/catissue/migration/migrator.rb
-- lib/catissue/migration/shims.rb
-- lib/catissue/migration/uniquify.rb
-- lib/catissue/util/controlled_value.rb
-- lib/catissue/util/location.rb
-- lib/catissue/util/log.rb
-- lib/catissue/util/person.rb
-- lib/catissue/util/position.rb
-- lib/catissue/util/storable.rb
-- lib/catissue/util/storage_type_holder.rb
-- History.txt
-- LEGAL
-- LICENSE
-- README.md
-rubygems_version: 1.3.7
 rdoc_options: []
 
-signing_key: 
-cert_chain: []
-
-name: caruby-tissue
-has_rdoc: yard
-platform: ruby
-summary: Ruby facade for caTissue.
-default_executable: 
-bindir: bin
-licenses: 
-- MIT
-required_rubygems_version: !ruby/object:Gem::Requirement 
+require_paths: 
+  - lib
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-  - - '>='
-    - !ruby/object:Gem::Version 
-      version: "0"
-      segments: 
-      - 0
-required_ruby_version: !ruby/object:Gem::Requirement 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
   requirements: 
-  - - '>='
-    - !ruby/object:Gem::Version 
-      version: "0"
-      segments: 
-      - 0
-require_paths: 
-- lib
-specification_version: 3
-test_files: []
-
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  type: :runtime
-  name: caruby-core
-  version_requirements: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version 
         version: "0"
-        segments: 
-        - 0
-  requirement: *id001
-description: "    The caruby-tissue gem applies the caRuby facade to the caTissue \
-  application.\n"
-email: caruby.org@gmail.com
-authors: 
-- OHSU
-extra_rdoc_files: []
-
 requirements: []
 
 rubyforge_project: caruby
-autorequire: 
+rubygems_version: 1.5.2
+signing_key: 
+specification_version: 3
+summary: Ruby facade for caTissue.
+test_files: []
+