caruby-tissue 1.5.6 → 2.1.1

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

@@ -1,50 +1,42 @@
-$:.unshift 'examples/galena/lib'
-
-require 'test/lib/catissue/test_case'
-require 'galena/tissue/seed/defaults'
+require File.dirname(__FILE__) + '/../helpers/test_case'
 
 # Verifies the Galena caTissue usage examples.
 class ExamplesTest < Test::Unit::TestCase
-  include CaTissue::TestCase
+  include Galena::TestCase
 
   def setup
     super
     @pcl = defaults.protocol
     @pcl.title = @pcl.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)
+    @pnt.add_mrn(defaults.hospital, Jinx::Uniquifier.qualifier)
+    solid = 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
+    @scg = @pcl.add_specimens(blood, solid, :participant => @pnt, :receiver => rcvr)
   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 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
@@ -58,13 +50,11 @@ class ExamplesTest < Test::Unit::TestCase
   # Verifies the Specimen relabel usage example.
   def test_site_specimens_relabel
     tb = defaults.tissue_bank
-    tb.name = tb_name = tb.name.uniquify
+    tbn = tb.name = tb.name.uniquify
     @scg.create
-    CaTissue::SpecimenCollectionGroup.new(:site => tb).query(:specimen_collection_group, :specimens).each do |spc|
+    CaTissue::SpecimenCollectionGroup.new(:site => tb).query(: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/tissue/helpers/test_case.rb

@@ -0,0 +1,24 @@
+require File.dirname(__FILE__) + '/../../../../../helpers/test_case'
+
+# Declare the ROOT_DIR constant before adding galena/lib to the Ruby path.
+
+module Galena
+  # The Galena example root directory.
+  ROOT_DIR = File.expand_path('galena', File.dirname(__FILE__) + '/../../../../../../examples')
+
+  module TestCase
+    include CaTissue::TestCase
+    
+    # Overrides the {CaTissue::TestCase} to reference the {Galena::Seed} defaults.
+    #
+    # @return [Seed] the test object fixture
+    def defaults
+      @defaults ||= Seed.new.uniquify
+    end
+  end
+end
+
+# Add galena/lib to the Ruby path.
+$:.unshift(Galena::ROOT_DIR + '/lib')
+
+require 'galena/seed'

metadata

@@ -2,7 +2,7 @@
 name: caruby-tissue
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 1.5.6
+  version: 2.1.1
 platform: ruby
 authors: 
   - OHSU
@@ -10,26 +10,91 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-30 00:00:00 -07:00
+date: 2012-04-13 00:00:00 -07:00
 default_executable: 
 dependencies: 
   - !ruby/object:Gem::Dependency 
-    name: caruby-core
+    name: bundler
     prerelease: false
     requirement: &id001 !ruby/object:Gem::Requirement 
       none: false
       requirements: 
         - - ">="
           - !ruby/object:Gem::Version 
-            version: 1.5.5
+            version: "0"
     type: :runtime
     version_requirements: *id001
-description: "    The caruby-tissue gem applies the caRuby facade to the caTissue application.\n"
+  - !ruby/object:Gem::Dependency 
+    name: jinx
+    prerelease: false
+    requirement: &id002 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: 2.1.1
+    type: :runtime
+    version_requirements: *id002
+  - !ruby/object:Gem::Dependency 
+    name: jinx-json
+    prerelease: false
+    requirement: &id003 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: 2.1.1
+    type: :runtime
+    version_requirements: *id003
+  - !ruby/object:Gem::Dependency 
+    name: uom
+    prerelease: false
+    requirement: &id004 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: 1.2.2
+    type: :runtime
+    version_requirements: *id004
+  - !ruby/object:Gem::Dependency 
+    name: yard
+    prerelease: false
+    requirement: &id005 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: "0"
+    type: :development
+    version_requirements: *id005
+  - !ruby/object:Gem::Dependency 
+    name: rake
+    prerelease: false
+    requirement: &id006 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: "0"
+    type: :development
+    version_requirements: *id006
+  - !ruby/object:Gem::Dependency 
+    name: rspec
+    prerelease: false
+    requirement: &id007 !ruby/object:Gem::Requirement 
+      none: false
+      requirements: 
+        - - ">="
+          - !ruby/object:Gem::Version 
+            version: "2.6"
+    type: :development
+    version_requirements: *id007
+description: Ruby facade for the caTissue application. See caruby.rubyforge.org for more information.
 email: caruby.org@gmail.com
 executables: 
   - crtdump
   - crtexample
-  - crtextract
   - crtmigrate
   - crtsmoke
 extensions: []
@@ -39,70 +104,59 @@ extra_rdoc_files: []
 files: 
   - bin/crtdump
   - bin/crtexample
-  - bin/crtextract
   - bin/crtmigrate
   - bin/crtsmoke
-  - conf/wustl/log4j.properties
+  - conf/wustl/linux/log4j.properties
+  - conf/wustl/windows/log4j.properties
+  - examples/galena/galena.gemspec
+  - examples/galena/Gemfile
+  - examples/galena/Gemfile.lock
+  - examples/galena/Rakefile
   - examples/galena/README.md
   - examples/galena/bin/seed
-  - examples/galena/conf/extract/simple_fields.yaml
-  - examples/galena/conf/migration/annotation_defaults.yaml
-  - examples/galena/conf/migration/annotation_fields.yaml
-  - examples/galena/conf/migration/filter_defaults.yaml
-  - examples/galena/conf/migration/filter_fields.yaml
-  - examples/galena/conf/migration/filter_values.yaml
-  - examples/galena/conf/migration/frozen_defaults.yaml
-  - examples/galena/conf/migration/frozen_fields.yaml
-  - examples/galena/conf/migration/general_fields.yaml
-  - examples/galena/conf/migration/participant_fields.yaml
-  - examples/galena/conf/migration/registration_fields.yaml
-  - examples/galena/conf/migration/simple_fields.yaml
+  - examples/galena/conf/defaults.yaml
+  - examples/galena/conf/annotation/defaults.yaml
+  - examples/galena/conf/annotation/fields.yaml
+  - examples/galena/conf/filter/fields.yaml
+  - examples/galena/conf/filter/values.yaml
+  - examples/galena/conf/frozen/defaults.yaml
+  - examples/galena/conf/frozen/fields.yaml
+  - examples/galena/conf/general/fields.yaml
+  - examples/galena/conf/registration/fields.yaml
+  - examples/galena/conf/simple/fields.yaml
   - examples/galena/data/annotation.csv
   - examples/galena/data/filter.csv
   - examples/galena/data/frozen.csv
   - examples/galena/data/general.csv
-  - examples/galena/data/participant.csv
   - examples/galena/data/registration.csv
   - examples/galena/data/simple.csv
   - examples/galena/lib/galena.rb
-  - examples/galena/lib/galena/tissue/migration/filter_shims.rb
-  - examples/galena/lib/galena/tissue/migration/frozen_shims.rb
-  - examples/galena/lib/galena/tissue/seed/defaults.rb
-  - examples/psbin/README.md
-  - examples/psbin/conf/adjuvant_hormone_defaults.yaml
-  - examples/psbin/conf/adjuvant_radiation_defaults.yaml
-  - examples/psbin/conf/biopsy_defaults.yaml
-  - examples/psbin/conf/biopsy_fields.yaml
-  - examples/psbin/conf/neoadjuvant_hormone_defaults.yaml
-  - examples/psbin/conf/neoadjuvant_radiation_defaults.yaml
-  - examples/psbin/conf/patient_defaults.yaml
-  - examples/psbin/conf/patient_fields.yaml
-  - examples/psbin/conf/surgery_defaults.yaml
-  - examples/psbin/conf/surgery_fields.yaml
-  - examples/psbin/conf/t_stage_defaults.yaml
-  - examples/psbin/conf/t_stage_fields.yaml
-  - examples/psbin/conf/therapy_fields.yaml
-  - examples/psbin/data/adjuvant_hormone.csv
-  - examples/psbin/data/adjuvant_radiation.csv
-  - examples/psbin/data/biopsy.csv
-  - examples/psbin/data/neoadjuvant_hormone.csv
-  - examples/psbin/data/neoadjuvant_radiation.csv
-  - examples/psbin/data/patient.csv
-  - examples/psbin/data/surgery.csv
-  - examples/psbin/data/t_stage.csv
-  - examples/psbin/lib/psbin/biopsy_shims.rb
-  - examples/psbin/lib/psbin/surgery_shims.rb
+  - examples/galena/lib/galena/filter.rb
+  - examples/galena/lib/galena/frozen.rb
+  - examples/galena/lib/galena/seed.rb
+  - examples/galena/lib/galena/version.rb
+  - examples/galena/log/galena.log
+  - examples/galena/log/galena.log.0
+  - examples/galena/spec/annotation_spec.rb
+  - examples/galena/spec/filter_spec.rb
+  - examples/galena/spec/frozen_spec.rb
+  - examples/galena/spec/general_spec.rb
+  - examples/galena/spec/registration_spec.rb
+  - examples/galena/spec/seed.rb
+  - examples/galena/spec/simple_spec.rb
+  - examples/galena/spec/spec_helper.rb
+  - examples/galena/spec/support/migration.rb
   - lib/catissue.rb
   - lib/catissue/database.rb
-  - lib/catissue/domain.rb
+  - lib/catissue/metadata.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/de_integration.rb
+  - lib/catissue/annotation/importer.rb
+  - lib/catissue/annotation/introspector.rb
+  - lib/catissue/annotation/metadata.rb
   - lib/catissue/annotation/proxy.rb
   - lib/catissue/annotation/proxy_1_1.rb
   - lib/catissue/annotation/proxy_class.rb
@@ -121,6 +175,7 @@ files:
   - lib/catissue/database/annotation/integrator.rb
   - lib/catissue/database/annotation/record_entry_integrator.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
@@ -142,7 +197,6 @@ files:
   - lib/catissue/domain/embedded_event_parameters.rb
   - lib/catissue/domain/external_identifier.rb
   - lib/catissue/domain/frozen_event_parameters.rb
-  - lib/catissue/domain/hash_code.rb
   - lib/catissue/domain/institution.rb
   - lib/catissue/domain/new_specimen_array_order_item.rb
   - lib/catissue/domain/order_details.rb
@@ -169,6 +223,13 @@ files:
   - lib/catissue/domain/participant/clinical/chemotherapy.rb
   - lib/catissue/domain/participant/clinical/duration.rb
   - lib/catissue/domain/participant/clinical/radiation_therapy.rb
+  - lib/catissue/domain/specimen/pathology/additional_finding.rb
+  - lib/catissue/domain/specimen/pathology/details.rb
+  - lib/catissue/domain/specimen/pathology/gleason_score.rb
+  - lib/catissue/domain/specimen/pathology/histologic_grade.rb
+  - lib/catissue/domain/specimen/pathology/histologic_type.rb
+  - lib/catissue/domain/specimen/pathology/histologic_variant_type.rb
+  - lib/catissue/domain/specimen/pathology/invasion.rb
   - lib/catissue/domain/specimen/pathology/prostate_specimen_gleason_score.rb
   - lib/catissue/domain/specimen/pathology/prostate_specimen_pathology_annotation.rb
   - lib/catissue/domain/specimen/pathology/specimen_additional_finding.rb
@@ -180,34 +241,30 @@ files:
   - lib/catissue/domain/specimen/pathology/specimen_invasion.rb
   - lib/catissue/domain/specimen_collection_group/pathology/base_pathology_annotation.rb
   - lib/catissue/domain/specimen_collection_group/pathology/base_solid_tissue_pathology_annotation.rb
-  - lib/catissue/extract/command.rb
-  - lib/catissue/extract/delta.rb
-  - lib/catissue/extract/extractor.rb
+  - lib/catissue/helpers/collectible.rb
+  - lib/catissue/helpers/collectible_event_parameters.rb
+  - lib/catissue/helpers/controlled_value.rb
+  - lib/catissue/helpers/hash_code.rb
+  - lib/catissue/helpers/location.rb
+  - lib/catissue/helpers/log.rb
+  - lib/catissue/helpers/person.rb
+  - lib/catissue/helpers/position.rb
+  - lib/catissue/helpers/properties_loader.rb
+  - lib/catissue/helpers/storable.rb
+  - lib/catissue/helpers/storage_type_holder.rb
   - lib/catissue/migration/migratable.rb
   - lib/catissue/migration/migrator.rb
   - lib/catissue/migration/shims.rb
-  - lib/catissue/migration/uniquify.rb
-  - lib/catissue/util/collectible.rb
-  - lib/catissue/util/collectible_event_parameters.rb
-  - lib/catissue/util/controlled_value.rb
-  - lib/catissue/util/location.rb
-  - lib/catissue/util/person.rb
-  - lib/catissue/util/position.rb
-  - lib/catissue/util/storable.rb
-  - lib/catissue/util/storage_type_holder.rb
-  - lib/catissue/util/uniquify.rb
+  - lib/catissue/migration/unique.rb
   - lib/catissue/wustl/logger.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/fixtures/lib/examples/galena/migration/alt_key_shims.rb
-  - test/lib/catissue/test_case.rb
+  - History.md
+  - LEGAL
+  - LICENSE
+  - README.md
+  - Gemfile
   - 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
@@ -221,6 +278,7 @@ files:
   - test/lib/catissue/domain/location_test.rb
   - test/lib/catissue/domain/participant_medical_identifier_test.rb
   - test/lib/catissue/domain/participant_test.rb
+  - test/lib/catissue/domain/received_event_parameters_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
@@ -234,26 +292,11 @@ files:
   - 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/catissue/helpers/properties_loader_test.rb
+  - test/lib/catissue/migration/helpers/test_case.rb
   - test/lib/examples/galena/tissue/domain/examples_test.rb
-  - test/lib/examples/galena/tissue/migration/annotation_test.rb
-  - test/lib/examples/galena/tissue/migration/filter_test.rb
-  - test/lib/examples/galena/tissue/migration/frozen_test.rb
-  - test/lib/examples/galena/tissue/migration/general_test.rb
-  - test/lib/examples/galena/tissue/migration/participant_test.rb
-  - test/lib/examples/galena/tissue/migration/registration_test.rb
-  - test/lib/examples/galena/tissue/migration/seedify.rb
-  - test/lib/examples/galena/tissue/migration/simple_test.rb
-  - test/lib/examples/galena/tissue/migration/test_case.rb
-  - test/lib/examples/psbin/migration_test.rb
-  - History.md
-  - LEGAL
-  - LICENSE
-  - README.md
-has_rdoc: true
+  - test/lib/examples/galena/tissue/helpers/test_case.rb
+has_rdoc: yard
 homepage: http://caruby.rubyforge.org/tissue.html
 licenses: 
   - MIT
@@ -274,12 +317,45 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - - ">="
       - !ruby/object:Gem::Version 
         version: "0"
-requirements: []
-
+requirements: 
+  - the caTissue API client
 rubyforge_project: caruby
 rubygems_version: 1.5.1
 signing_key: 
 specification_version: 3
-summary: Ruby facade for caTissue.
-test_files: []
-
+summary: Ruby facade for the caTissue application
+test_files: 
+  - 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/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/external_identifier_test.rb
+  - test/lib/catissue/domain/location_test.rb
+  - test/lib/catissue/domain/participant_medical_identifier_test.rb
+  - test/lib/catissue/domain/participant_test.rb
+  - test/lib/catissue/domain/received_event_parameters_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/helpers/properties_loader_test.rb
+  - test/lib/catissue/migration/helpers/test_case.rb
+  - test/lib/examples/galena/tissue/domain/examples_test.rb
+  - test/lib/examples/galena/tissue/helpers/test_case.rb