caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/version.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # The version of this caRuby Tissue release.
-  VERSION = "1.5.6"
+  VERSION = "2.1.1"
   
   # The supported caTissue release versions.
   CATISSUE_VERSIONS = "1.1.2-1.2"

data/lib/catissue/wustl/logger.rb

@@ -1,61 +1,81 @@
+require 'fileutils'
+require 'jinx/helpers/os'
+
 # Wustl wraps the +edu.wustl+ package.
 module Wustl
   # Logger configures the +edu.wustl+ logger.
   module Logger
+    # @quirk caTissue caTissue requires that the log file parent directory exists.
+    #   Messages are logged to +client.log+ and +catissuecore.log+ in this directory. If the
+    #   directory does not exist, then caTissue raises a FileNotFound exception. The exception
+    #   message indicates the log file rather than the log directory. This message is misleading,
+    #   since the problem is not that the log file is not found but that the log directory does
+    #   not exist. The work-around is to detect the log file from the log4j properties and ensure
+    #   that the parent directory exists.
+    #
     # @quirk caTissue the caTissue logger must be initialized before caTissue objects are created.
     #   The logger at issue is the caTissue client logger, not the caTissue server logger nor
     #   the caRuby logger. The caTissue logger facade class is edu.wustl.common.util.logger.Logger.
     #   In caTissue 1.1.x, initialization is done with +configure+, in 1.2 with
     #   +LoggerConfig.configureLogger+.
     #
-    # @quirk catTissue +LoggerConfig.configureLogger+ expects file +log4j.properties+ in the class
-    #   path. However, in 1.2 the client property file is +client_log4j.properties+. Work-around is
-    #   as follows:
-    #   * copy this file into the caRuby Tissue distribution as +conf/wustl/log4.properties+
-    #   * add +conf/wustl+ to the classpath.
-    #   * call +LoggerConfig.configureLogger+ with the config directory as an argument
+    # @quirk catTissue 1.2 +LoggerConfig.configureLogger+ expects file +log4j.properties+ in the
+    #   classpath. However, in 1.2 the client property file is +client_log4j.properties+. The
+    #   work-around is to configure an empty log if there is no +log4j.properties+ in the classpath.
     #
-    # @quirk caTissue The caTissue client log location is unfortunately hard-coded in a caTissue client
+    # @quirk caTissue caTissue ignores the +client.log+ and +catissuecore.log+ log level set in
+    #   the client jar +log4j.properties+. caTissue spews forth copious cryptic comments,
+    #   regardless of the log level.
+    #
+    # @quirk caTissue 1.1.1 The caTissue client log location is unfortunately hard-coded in a caTissue
     #   configuration file, does not create the parent directory on demand, and issues an obscure error
-    #   message if the directory does not exist in release 1.1.x. The work-around is to ensure that the
-    #   working directory contains a log subdirectory.
+    #   client message if the directory does not exist. The work-around is to ensure that the working
+    #   directory contains a log subdirectory.
     def self.configure
       # Set the configured flag. Configure only once.
       if @configured then return else @configured = true end
-      # make the required log subdirectory in the working directory
-      ensure_log_directory_exists
-      # the caTissue 1.1.x mechanism
+      # the log4j properties
+      props = Java.load_properties('log4j.properties')
+      
+      # Ensure that the parent directory exists.
+      if props then
+        clt_log = props['log4j.appender.clientLog.File']
+        ensure_parent_directory_exists(clt_log) if clt_log
+        core_log = props['log4j.appender.catissuecoreclientLog.File']
+        ensure_parent_directory_exists(core_log) if core_log
+      end
+      
+      # The logger is configured differently depending on the caTissue version.
       log_cls = Java::edu.wustl.common.util.logger.Logger
       if log_cls.respond_to?(:configure) then
+        # the caTissue 1.1.2 mechanism
         log_cls.configure("")
       else
         # the caTissue 1.2 mechanism
         cfg_cls = Java::edu.wustl.common.util.logger.LoggerConfig
-        dir = File.join(File.dirname(__FILE__), '..', '..', '..', 'conf', 'wustl')
+        # the caTissue 1.2 work-around
+        dir = clt_log ? File.dirname(clt_log) : default_log4j_config_directory
+        # configure the logger
         cfg_cls.configureLogger(dir)
       end
     end
-  
+    
     private
-
-    # Makes a +./log+ subdirectory to avoid a caTissue log initializer error. This method should be called
-    # before configuring the logger.
+    
+    CONF_DIR = File.dirname(__FILE__) + '/../../../conf/wustl'
+    
+    # Creates the parent directory of the given target path, if necessary.
     #
-    # @quirk caTissue avoid caTissue error by creating log subdirectory.
-    def self.ensure_log_directory_exists
-      if File.directory?('log') then
-        unless File.writable?('log') then
-          raise StandardError.new("caTissue log subdirectory #{File.expand_path('log')} is not writable")
-        end
-      elsif File.exists?('log') then
-        raise StandardError.new("Existing file #{File.expand_path('log')} prevents creation of the required caTissue log subdirectory")
-      else
-        begin
-          Dir.mkdir('log')
-        rescue Exception => e
-          raise StandardError.new("Cannot create the log subdirectory required by the caTissue client: #{File.expand_path('log')}")
-        end
-      end
+    # @param [String] path the target path
+    def self.ensure_parent_directory_exists(path)
+      return if path == '/dev/null' or path == 'NUL'
+      File.mkdir(File.dirname(path))
+    end
+    
+    # @return [String] the log4j config to use if one is not found in the classpath
+    def self.default_log4j_config_directory
+      subdir = Jinx::OS.os_type == :windows ? 'windows' : 'linux'
+      File.expand_path(subdir, CONF_DIR)
     end
   end
 end

data/lib/catissue.rb

@@ -1,25 +1,43 @@
-# This file is the entry point included by applications which reference a CaTissue object or service.
+# This file is the entry point included by applications which use a CaTissue application service.
+require 'uom'
+require 'jinx'
+require 'jinx/json'
+require 'jinx/json/serializer'
+require 'caruby'
+require 'catissue/resource'
+require 'catissue/metadata'
+require 'catissue/annotation/annotatable'
+require 'catissue/helpers/properties_loader'
 
-# the caRuby core gem
-require 'rubygems'
-begin
-  gem 'caruby-core'
-rescue LoadError
-  # if the gem is not available, then try a local development source
-  $:.unshift File.join(File.dirname(__FILE__), '..', '..', 'caruby', 'lib')
-end
+# The caTissue domain package metadata mix-in. Each domain class automatically
+# includes this CaTissue module when it is referenced.
+module CaTissue
+  include Annotatable, Resource
+  
+  extend Jinx::Importer
 
-require 'caruby/util/log'
-require 'catissue/domain'
-require 'catissue/database'
+   # Each CaTissue domain class extends CaTissue::Metadata.
+   @metadata_module = Metadata
+  
+  # Inject the importer and application properties loader into this CaTissue module.
+  extend PropertiesLoader
 
-# CaTissue wraps the caTissue Java API.
-# See the caRuby[http://http://caruby.rubyforge.org/] home page for more information.
-module CaTissue
-  # @param [<String>] nodes the path components relative to the caRuby Tissue source directory
-  # @return [String] the file path to the specified path components
-  def self.path(*nodes)
-    root = File.join(File.dirname(__FILE__), '..')
-    File.expand_path(File.join(*nodes), root)
+  # The caTissue Java package name.
+  packages 'edu.wustl.catissuecore.domain', 'edu.wustl.common.domain'
+  
+  # The JRuby mix-ins are in the domain subdirectory.
+  definitions File.dirname(__FILE__) + '/catissue/domain'
+  
+  private
+  
+  # Augments the superclass +Jinx::Importer.configure_importer+ method to first load
+  # the properties, build the classpath and initialize the caTissue logger.
+  def self.configure_importer
+    # Load the properties on demand.
+    properties
+    # Work around the caTissue logger bug.
+    require 'catissue/helpers/log'
+    # Delegate to superclass for the heavy lifting.
+    super
   end
 end

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

@@ -1,38 +1,33 @@
-$:.unshift 'lib'
-$:.unshift '../caruby/lib'
-
-require "test/unit"
-require 'caruby/util/log'
-require 'caruby/util/uniquifier'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/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)
+  def test_search_by_public_id
+    races = CaTissue::ControlledValues.instance.for_public_id('Race_PID')
+    assert_not_nil(races, "Race CVs not loaded")
+    assert_not_nil(races.detect { |cv| cv.value == 'White' }, "Race not found")
   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")
+    cv = CaTissue::ControlledValues.instance.find(:tissue_site, 'Esophagus, NOS')
+    assert_not_nil(cv, "'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")
+    cv = CaTissue::ControlledValues.instance.find(:tissue_site, 'esophagus, NOS')
+    assert_not_nil(cv, "Case-insensitive look-up inoperative")
+  end
+
+  def test_find_recursive
+    root = CaTissue::ControlledValues.instance.find(:tissue_site, 'DIGESTIVE ORGANS', true)
+    assert_not_nil(root, "'DIGESTIVE ORGANS' CV not found")
+    assert(!root.children.empty?, "#{root} missing children")
+    stomach = root.children.detect { |cv| cv.value == 'STOMACH' }
+    assert_not_nil(stomach, "#{root} STOMACH child CV not found")
+    pylorus = stomach.children.detect { |cv| cv.value == 'Pylorus' }
+    assert_not_nil(pylorus, "#{pylorus} Pylorus child CV not found")
+    assert(stomach.descendants.include?(pylorus), "#{root} CV missing #{pylorus} descendant")
   end
 
   def test_create_delete
@@ -44,4 +39,4 @@ class ControlledValuesTest < Test::Unit::TestCase
     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
+end

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

@@ -0,0 +1,18 @@
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+
+module CaTissue
+  class DatabaseTest < Test::Unit::TestCase
+    def test_executor
+      assert_nothing_raised("Executor execute failed") do
+        CaTissue::Database.instance.executor.execute { |dbh| dbh.execute(SQL) }
+      end
+      assert_nothing_raised("Executor query failed") do
+        CaTissue::Database.instance.executor.query(SQL)
+      end
+    end
+  
+    private
+  
+    SQL = "select count(*) from catissue_site"
+  end
+end

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

@@ -1,5 +1,5 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/util/uniquifier'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/uniquifier'
 
 class AddressTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -10,6 +10,10 @@ class AddressTest < Test::Unit::TestCase
     @user = defaults.tissue_bank.coordinator
     @addr = @user.address
   end
+  
+  def test_primary_key
+    assert_equal([:identifier], CaTissue::Address.primary_key_attributes, "Primary key is not the identifier")
+  end
 
   def test_defaults
     verify_defaults(@addr)
@@ -21,13 +25,7 @@ class AddressTest < Test::Unit::TestCase
   end
 
   def test_save
-    # Create the address.
-    verify_save(@addr)
-    # Modify the address.
-    expected = @addr.street = "#{Uniquifier.qualifier} Elm"
-    verify_save(@addr)
-    # Find the address.
-    fetched = @addr.copy(:identifier).find
-    assert_equal(expected, fetched.street, "Address street not saved")
+    # Address cannot be created.
+    assert_raises(CaRuby::DatabaseError, "Address create is incorrectly allowed.") { @addr.create }
   end
-end
+end

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

@@ -1,26 +1,15 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class CaTissueTestDefaultsTest < Test::Unit::TestCase
   include CaTissue::TestCase
 
-  attr_reader :defaults
-
-  def setup
-    super
-    @defaults = CaTissueTest::Defaults.instance
-  end
-
+  # Validates the #{CaTissue::TestCase::Seed} data.
   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) } }
+    assert_nothing_raised(Jinx::ValidationError, "Defaults validation unsuccessful") { defaults.add_defaults.validate }
   end
 
-  # Store the test data
+  # Saves the #{CaTissue::TestCase::Seed} data.
   def test_save
-    defaults.each { |obj| verify_save(obj) }
+    defaults.domain_objects.each { |obj| verify_save(obj) }
   end
 end

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

@@ -1,9 +1,9 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class CapacityTest < Test::Unit::TestCase
   include CaTissue::TestCase
 
-  # Verifies the :rows and :columns aliases.
+  # 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")

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

@@ -1,5 +1,5 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
-require 'caruby/util/validation'
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
+require 'jinx/helpers/validation'
 
 class CollectionEventParametersTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -10,13 +10,21 @@ class CollectionEventParametersTest < Test::Unit::TestCase
     @spc = defaults.specimen
   end
   
-  def test_scg_owner_conflict
-    assert_raises(ValidationError, "Owner conflict allowed") { @scg.received_event_parameters.specimen = @spc }
+  def test_specimen_inverse_integrity
+    # A default CEP is added to a specimen.
+    @spc.add_defaults
+    cep = @spc.collection_event_parameters
+    assert_same(@spc, cep.specimen, "#{cep} not added to #{@spc} event parameters")
+  end
+  
+  def test_scg_inverse_integrity
+    cep = @scg.collection_event_parameters
+    assert_same(@scg, cep.specimen_collection_group, "#{cep} not added to #{@scg} event parameters")
   end
   
-  def test_specimen_owner_conflict
-    @spc.collect(:receiver => @scg.receiver)
-    assert_raises(ValidationError, "Owner conflict allowed") { @spc.received_event_parameters.specimen_collection_group = @scg }
+  def test_owner_conflict
+    cep = CaTissue::SpecimenEventParameters.create_parameters(:collection, @scg)
+    assert_raises(Jinx::ValidationError, "Conflict allowed") { cep.specimen = @spc }
   end
   
   def test_update_scg_cep
@@ -30,7 +38,7 @@ class CollectionEventParametersTest < Test::Unit::TestCase
   end
   
   def test_update_specimen_cep
-    assert_nothing_raised("#{@scg} not created") { database.create(@spc) }
+    assert_nothing_raised("#{@spc} not created") { database.create(@spc) }
     cep = @spc.collection_event_parameters
     assert_not_nil(cep, "Autogenerated #{@spc} CEP not found")
     assert_not_nil(cep.identifier, "Autogenerated #{@spc} CEP identifier not set")

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

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class CollectionProtocolEventTest < Test::Unit::TestCase
   include CaTissue::TestCase

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

@@ -1,4 +1,4 @@
-require File.join(File.dirname(__FILE__), '..', 'test_case')
+require File.dirname(__FILE__) + '/../../../helpers/test_case'
 
 class CollectionProtocolRegistrationTest < Test::Unit::TestCase
   include CaTissue::TestCase
@@ -11,52 +11,62 @@ class CollectionProtocolRegistrationTest < Test::Unit::TestCase
   def test_defaults
     verify_defaults(@reg)
   end
-
+  
   def test_missing_ppi_defaults
     @reg.protocol_participant_identifier = nil
     verify_defaults(@reg)
   end
-
+  
   def test_inverse_protocol
     assert(@reg.protocol.registrations.include?(@reg), "Registration not included in protocol registrations")
   end
-
+  
+  def test_inverse_scgs
+    assert(!@reg.specimen_collection_groups.empty?, "#{@reg} SCG is missing.")
+  end
+  
   # Tests whether the registration date can be set to either a Ruby or a Java Date and always return a Ruby Date.
   def test_registration_date
     value = DateTime.now
     @reg.registration_date = value
     assert_equal(value.to_s, @reg.registration_date.to_s, "Registration date incorrect")
   end
-
+  
   def test_numeric_identifier
     @reg.protocol_participant_identifier = 1
     assert_equal("1", @reg.protocol_participant_identifier)
   end
-
+  
   def test_disable
     # add a derived specimen
-    specimen = @reg.specimens.first
-    child = specimen.derive(:specimen_class => :molecular, :specimen_requirement => defaults.specimen_requirement)
-    attributes = [:specimen_collection_groups, :specimens, :child_specimens]
-    @reg.visit_path(attributes) { |obj| obj.activity_status = 'Disabled' }
-    assert_equal('Disabled', @reg.activity_status, "Registration not disabled")
-    @reg.specimen_collection_groups.each { |scg| assert_equal('Disabled', scg.activity_status, "SCG #{scg} not disabled") }
-    @reg.specimens.each { |spc| assert_equal('Disabled', spc.activity_status, "Specimen #{spc} not disabled") }
+    spc = @reg.specimens.first
+    assert_not_nil(spc, "#{@reg} specimen missing")
+    child = spc.derive(:specimen_class => :molecular, :specimen_requirement => defaults.specimen_requirement)
+    @reg.visit_path(:specimen_collection_groups, :specimens, :child_specimens) do |ref|
+      ref.activity_status = 'Disabled'
+    end
+    assert_equal('Disabled', @reg.activity_status, "#{@reg} not disabled")
+    @reg.specimen_collection_groups.each do |scg|
+      assert_equal('Disabled', scg.activity_status, "#{scg} not disabled")
+    end
+    @reg.specimens.each do |rspc|
+      assert_equal('Disabled', rspc.activity_status, "#{rspc} not disabled")
+    end
     assert_equal('Disabled', child.activity_status, "Child Specimen #{child} not disabled")
   end
-
+  
   # Tests creating and fetching a registration.
   def test_save
     # store the registration without an SCG
     @reg.specimen_collection_groups.clear
     verify_save(@reg)
-
+  
     # an SCG should be auto-generated
     scg = @reg.specimen_collection_groups.first
     assert_not_nil(scg, "Missing auto-generated SCG")
     # the SCG status is pending
     assert_equal('Pending', scg.collection_status, "Auto-generated SCG collection status incorrect")
-
+  
     # modify the consent status and update
     rsps = @reg.consent_tier_responses
     assert_equal(1, rsps.size, "Consent tier responses size incorrect")