caruby-tissue 1.5.6 → 2.1.1

data/test/lib/examples/psbin/migration_test.rb

@@ -1,153 +0,0 @@
-# Borrow the Galena test apparatus.
-require 'test/lib/examples/galena/tissue/migration/test_case'
-
-# Tests the PSBIN example migration.
-module PSBIN
-  class MigrationTest < Test::Unit::TestCase
-    include Galena::Tissue::MigrationTestCase
-    
-    def setup
-      super(FIXTURES)
-    end
-
-    def test_patient_target
-      verify_target(:patient, PATIENT_OPTS)
-    end
-
-    def test_biopsy_target
-      verify_target(:biopsy, BIOPSY_OPTS)
-    end
-
-    def test_surgery_target
-      verify_target(:surgery, SURGERY_OPTS)
-    end
-    
-    def test_t_stage_target
-      verify_target(:t_stage, T_STAGE_OPTS)
-    end
-    
-    def test_adj_hormone_target
-      verify_target(:adjuvant_hormone, ADJ_HORMONE_OPTS) 
-    end
-    
-    def test_adj_radiation_target
-      verify_target(:adjuvant_radiation, ADJ_RAD_OPTS) 
-    end
-    
-    def test_neoadj_hormone_target
-      verify_target(:neoadjuvant_hormone, NEOADJ_HORMONE_OPTS) 
-    end
-    
-    def test_neoadj_radiation_target
-      verify_target(:neoadjuvant_radiation, NEOADJ_RAD_OPTS) 
-    end
-    
-    ## DATABASE TEST CASES ##
-
-    # Tests saving the biopsy, prostatectomy and associated annotations for a single patient.
-    # Note that saving the patient first results in an extra caTissue junk anticipated SCG,
-    # since the patient migration does not create an SCG and therefore cannot fill in the
-    # anticipated SCG. Otherwise, the migrations can be run in any order with the same
-    # result.
-    #
-    # NOTE: Occasionally a test case fails sporadically when run as a suite. Testing individually succeeds.
-    # Presumably a test artifact. TODO - isolate. 1.1.2 only?
-
-    def test_save_biopsy
-      logger.debug { "#{qp} saving biopsy SCG..." }
-      verify_save(:biopsy, BIOPSY_OPTS)
-    end
-    
-    def test_save_surgery
-      logger.debug { "#{qp} saving surgery SCG..." }
-      verify_save(:surgery, SURGERY_OPTS)
-    end
-
-    def test_save_patient
-      logger.debug { "#{qp} saving patient..." }
-      verify_save(:patient, PATIENT_OPTS)
-    end
-    
-    def test_save_tstage
-      logger.debug { "#{qp} saving T Stage..." }
-      verify_save(:t_stage, T_STAGE_OPTS)
-    end
-    
-    def test_save_adjuvant_hormone
-      logger.debug { "#{qp} saving adjuvant hormone therapy..." }
-      verify_save(:adjuvant_hormone, ADJ_HORMONE_OPTS)
-    end
-    
-    def test_save_adjuvant_radiation
-      logger.debug { "#{qp} saving adjuvant radiation therapy..." }
-      verify_save(:adjuvant_radiation, ADJ_RAD_OPTS)
-    end
-    
-    def test_save_neoadjuvant_hormone
-      logger.debug { "#{qp} saving neoadjuvant hormone therapy..." }
-      verify_save(:neoadjuvant_hormone, NEOADJ_HORMONE_OPTS)
-    end   
-    
-    def test_save_neoadjuvant_radiation
-      logger.debug { "#{qp} saving neoadjuvant radiation therapy..." }
-      verify_save(:neoadjuvant_radiation, NEOADJ_RAD_OPTS)
-    end
-    
-    private
-  
-    # The default migration input data directory.
-    FIXTURES = 'examples/psbin/data'
-  
-    # The default migration shims directory.
-    SHIMS = 'examples/psbin/lib/psbin'
-    
-    # The dfault migration configuration directory.
-    CONFIGS = 'examples/psbin/conf'
-    
-    PATIENT_OPTS = {
-      :target => CaTissue::Participant,
-      :mapping => File.join(CONFIGS, 'patient_fields.yaml'),
-      :defaults => File.join(CONFIGS, 'patient_defaults.yaml'),
-    }
-    
-    BIOPSY_OPTS = {
-      :target => CaTissue::SpecimenCollectionGroup,
-      :mapping => File.join(CONFIGS, 'biopsy_fields.yaml'),
-      :defaults => File.join(CONFIGS, 'biopsy_defaults.yaml'),
-      :shims => [File.join(SHIMS, 'biopsy_shims.rb')]
-    }
-    
-    SURGERY_OPTS = {
-      :target => CaTissue::SpecimenCollectionGroup,
-      :mapping => File.join(CONFIGS, 'surgery_fields.yaml'),
-      :defaults => File.join(CONFIGS, 'surgery_defaults.yaml'),
-      :shims => [File.join(SHIMS, 'surgery_shims.rb')]
-    }
-    
-    T_STAGE_OPTS = {
-      :target => CaTissue::Participant::Clinical::LabAnnotation,
-      :mapping => File.join(CONFIGS, 't_stage_fields.yaml'),
-      :defaults => File.join(CONFIGS, 't_stage_defaults.yaml'),
-    }
-    
-    def self.therapy_options(timing, agent)
-      target = case agent
-        when :hormone then CaTissue::Participant::Clinical::TreatmentAnnotation
-        when :radiation then CaTissue::Participant::Clinical::RadRXAnnotation
-      end
-      {
-        :target => target,
-        :mapping => File.join(CONFIGS, 'therapy_fields.yaml'),
-        :defaults => File.join(CONFIGS, "#{timing}_#{agent}_defaults.yaml")
-      }
-    end
-    
-    ADJ_HORMONE_OPTS = therapy_options(:adjuvant, :hormone)
-    
-    ADJ_RAD_OPTS = therapy_options(:adjuvant, :radiation)
-    
-    NEOADJ_HORMONE_OPTS = therapy_options(:neoadjuvant, :hormone)
-    
-    NEOADJ_RAD_OPTS = therapy_options(:neoadjuvant, :radiation)
-  end
-end