caruby-tissue 1.5.6 → 2.1.1

data/lib/catissue/annotation/proxy.rb

@@ -4,12 +4,12 @@ module CaTissue
     module Proxy
       # @return [Annotatable] the annotated domain object  
       def hook
-        send(self.class.owner_attribute_metadata.reader)
+        send(self.class.owner_property.reader)
       end
       
       # @param [Annotatable] obj the domain object to annotate  
       def hook=(obj)
-        send(self.class.owner_attribute_metadata.writer, obj)
+        send(self.class.owner_property.writer, obj)
       end
       
       # Ensures that this proxy's hook exists in the database.

data/lib/catissue/annotation/proxy_class.rb

@@ -1,6 +1,7 @@
 require 'set'
-require 'caruby/util/collection'
-require 'caruby/util/partial_order'
+require 'jinx/helpers/collections'
+
+require 'jinx/helpers/partial_order'
 require 'catissue/annotation/annotation'
 require 'catissue/annotation/proxy_1_1'
 require 'catissue/annotation/record_entry_proxy'
@@ -9,6 +10,9 @@ module CaTissue
   module Annotation
     # Annotation hook proxy class mix-in.
     module ProxyClass
+      # @return [CaRuby::Property] the hook class attribute meta-data for this proxy
+      attr_reader :hook_property
+      
       # @param [Class] klass the proxy class
       def self.extended(klass)
         super
@@ -17,55 +21,67 @@ module CaTissue
         klass.class_eval { include mixin }
       end
       
-      # @return [AnnotatableClass] the hook class for this proxy
+      # @return [Metadata] the hook class for this proxy
       def hook
-        owner_type
+        hook_property.type
       end
       
       # Sets this proxy's hook to the given class and creates the
       # proxy => hook attribute with the given hook => proxy inverse.
       #
-      # @param [AnnotatableClass] klass the annotated domain object class
+      # @param [Metadata] klass the annotated domain object class
       def hook=(klass)
         # Make a new hook reference attribute.
-        attr = klass.name.demodulize.underscore
-        attr_accessor(attr)
+        pa = klass.name.demodulize.underscore
+        attr_accessor(pa)
         # The attribute type is the given hook class.
-        add_attribute(attr, klass)
-        logger.debug { "Added #{klass.qp} annotation proxy => hook attribute #{attr}." }
+        @hook_property = add_attribute(pa, klass)
+        logger.debug { "Added #{klass.qp} annotation proxy => hook attribute #{pa}." }
       end
       
       # Adds each proxy => annotation reference as a dependent attribute.
       # Recursively adds dependents of all referenced annotations.
+      #
+      # This method defines a proxy attribute in each primary annotation class
+      # for each {#non_proxy_annotation_classes} class hierarchy.
       def build_annotation_dependency_hierarchy
         logger.debug { "Building annotation dependency hierarchy..." }
         non_proxy_annotation_classes.each do |klass|
-          klass.annotation_hierarchy.each do |anc|
-            if anc.primary? and anc.proxy_attribute.nil? then
-              anc.define_proxy_attribute(self)
-            end
-          end
-          logger.info(klass.pp_s)
+          ensure_primary_references_proxy(klass)
         end
         set_inverses
         add_dependent_attributes
         add_dependent_attribute_closure
       end
       
+      # Ensures that the given primary class references this proxy.
+      #
+      # @param [Metadata] klass the primary annotation class to check
+      def ensure_primary_references_proxy(klass)
+        # Define the superclass proxy attributes, starting with the most general class.
+        klass.annotation_hierarchy.to_a.reverse_each do |anc|
+          if anc.primary? and anc.proxy_attribute.nil? then
+            anc.define_proxy_attribute(self)
+          end
+        end
+      end
+      
       # Creates a reference attribute from this proxy to the given primary {Annotation} class. 
       #
-      # @param [Class] klass the annotation class
+      # @param [Class] klass the target annotation class
+      # @return [Symbol] the new annotation reference attribute
       def create_annotation_attribute(klass)
         # the new attribute symbol
-        attr = klass.name.demodulize.underscore.pluralize.to_sym
-        logger.debug { "Creating annotation proxy #{qp} attribute #{attr} to hold primary annotation #{klass.qp} instances..." }
+        pa = klass.name.demodulize.underscore.pluralize.to_sym
+        logger.debug { "Creating annotation proxy #{qp} attribute #{pa} to hold primary annotation #{klass.qp} instances..." }
         # Define the access methods: the reader creates a new set on demand to hold the annotations.
-        attr_create_on_demand_accessor(attr) { Set.new }
+        attr_create_on_demand_accessor(pa) { Set.new }
         # add the annotation collection attribute
-        add_attribute(attr, klass, :collection)
+        add_attribute(pa, klass, :collection)
         # The annotation is dependent.
-        add_dependent_attribute(attr, :logical)
-        attr
+        add_dependent_attribute(pa, :logical)
+        logger.debug { "Created annotation proxy #{qp} dependent attribute #{pa}." }
+        pa
       end
       
       private
@@ -79,18 +95,17 @@ module CaTissue
         # The inverse is the direct, unwrapped proxy reference named by the annotation module.
         inv = annotation_module.name.demodulize.underscore.to_sym
         # The attributes in class hierarchy general-to-specific order
-        attr_mds = annotation_attributes.enum_metadata.partial_sort_by { |attr_md| attr_md.type }.reverse
-        logger.debug { "Setting #{self} inverses for annotation attributes #{attr_mds.to_series}." }
-        attr_mds.each do |attr_md|
-          attr_md.type.define_proxy_attribute(self)
-          set_attribute_inverse(attr_md.to_sym, inv)
+        props = annotation_attributes.properties.partial_sort_by { |prop| prop.type }.reverse
+        logger.debug { "Setting #{self} inverses for annotation attributes #{props.to_series}." }
+        props.each do |prop|
+          prop.type.define_proxy_attribute(self)
+          set_attribute_inverse(prop.to_sym, inv)
         end
       end
       
-      # @return <AnnotationClass> the non-proxy annotation classes
+      # @return <Metadata> the non-proxy annotation classes
       def non_proxy_annotation_classes
-        consts = annotation_module.constants.map { |s| annotation_module.const_get(s) }
-        consts.select { |c| Class === c and c < Annotation and not c < Proxy }
+        annotation_module.annotation_classes.filter { |klass| not klass < Proxy }
       end
     end
   end

data/lib/catissue/annotation/record_entry_proxy.rb

@@ -8,12 +8,12 @@ module CaTissue
       
       # @return [Annotatable] the annotated domain object  
       def hook
-        send(self.class.owner_attribute_metadata.reader)
+        send(self.class.owner_property.reader)
       end
       
       # @param [Annotatable] obj the domain object to annotate  
       def hook=(obj)
-        send(self.class.owner_attribute_metadata.writer, obj)
+        send(self.class.owner_property.writer, obj)
       end
     end
   end

data/lib/catissue/cli/command.rb

@@ -1,30 +1,19 @@
-# the standard log file
-DEF_LOG_FILE = 'log/catissue.log' unless defined?(DEF_LOG_FILE)
-
-begin
-  require 'catissue'
-rescue Exception => e
-  logger.error("caTissue client load was unsuccessful - #{e}:\n#{e.backtrace.qp}")
-  puts "caTissue client load was unsuccessful - #{e}."
-  puts "See the log at #{CaRuby::Log.instance.file} for more information."
-  exit 1
-end
-
-require 'caruby/cli/command'
-require 'catissue/version'
+require 'jinx/cli/command'
+require 'catissue'
+# defined check below guards against bundle exec redundant version.rb load.
+require 'catissue/version' unless CaTissue.const_defined?('VERSION')
+require 'caruby/database'
 
 module CaTissue
   module CLI
-    # Augments {CaRuby::CLI::Command} with caTissue-specific command line option handlers.
-    class Command < CaRuby::CLI::Command
-      # 
+    # Augments +CaRuby::CLI::Command+ with caTissue-specific command line option handlers.
+    class Command < Jinx::CLI::Command
       # Built-in options include those specified in +CaRuby::CLI::Command.initialize+
       # as well as the following:
-      # * --version : print the version of caRuby Tissue as well as the supported caTissue releases and exit
+      # * +--version+ : print the version of caRuby Tissue as well as the supported
+      #   caTissue releases and exit
       #
-      # @param [(<Symbol>, <String, Class>)] specs the arguments and options
-      #   described in +CaRuby::CLI::Command.initialize+
-      # @see {CaRuby::CLI::Command#initialize}
+      # @param (see CaRuby::CLI::Command#initialize)
       def initialize(specs=[])
         specs << VERSION_OPT
         super
@@ -43,10 +32,11 @@ module CaTissue
         super
         if opts[:version] then
           puts "#{CaTissue::VERSION} for caTissue v#{CaTissue::CATISSUE_VERSIONS}"
-        else
-          CaRuby::ACCESS_OPTS.each do |opt, *spec|
+          exit 0
+        elseuniqurify
+          CaRuby::Database::ACCESS_OPTS.each do |opt, *spec|
             value = opts.delete(opt)
-            CaTissue.access_properties[opt] = value if value
+            CaTissue.properties[opt] = value if value
           end
         end
       end

data/lib/catissue/cli/example.rb

@@ -1,5 +1,6 @@
-require 'catissue/cli/command'
-require 'caruby/util/collection'
+require File.dirname(__FILE__) + '/command'
+require 'jinx/helpers/collections'
+
 
 module CaTissue
   module CLI
@@ -16,7 +17,8 @@ module CaTissue
   
       # Lists the examples.
       def list
-        root = CaTissue.path('examples')
+        root = File.expand_path('examples', File.dirname(__FILE__) + '/../../..')
+        raise RuntimeError.new("Examples directory not found: #{root}") unless File.exists?(root)
         Dir.foreach(root) do |f|
           path = File.expand_path(f, root)
           if File.directory?(path) and f[0, 1] != '.' then

data/lib/catissue/cli/migrate.rb

@@ -1,7 +1,4 @@
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-
-require 'catissue/cli/command'
+require File.dirname(__FILE__) + '/command'
 require 'catissue/migration/migrator'
 
 module CaTissue
@@ -9,52 +6,63 @@ module CaTissue
     class Migrate < Command
       # The migration option specifications.
       #
-      # The :unique option ensures that the migrated objects do not conflict with existing or future
+      # The +:unique+ option ensures that the migrated objects do not conflict with existing or future
       # objects. This is used for testing a migration dry run. It is recommended that the trial run
       # protocol is set to a test protocol as well.
       SPECS = [
-        [:input, "input", "Source file to migrate"],
-        [:target, "-t", "--target CLASS", "Migration target class"],
-        [:mapping, "-m", "--mapping FILE[,FILE...]", Array, "The input field => caTissue attribute mapping file(s)"],
-        [:filters, "--filters FILE[,FILE...]", Array, "The input value => caTissue value mapping file(s)"],
-        [:defaults, "-d", "--defaults FILE[,FILE...]", Array, "The caTissue attribute default value file(s)"],
-        [:shims, "-s", "--shims FILE[,FILE...]", Array, "Migration customization shim file(s) to load"],
-        [:bad, "-b", "--bad FILE", "Write each invalid record to the given file and continue migration"],
-        [:unique, "-u", "--unique", "Make the migrated objects unique for testing"],
-        [:offset, "-o", "--offset N", Integer, "Number of input records to skip before starting the migration"]
+        [:input, 'INPUT', 'Source file to migrate'],
+        [:target, '-t', '--target CLASS', 'Migration target class'],
+        [:mapping, '-m', '--mapping FILE[,FILE...]', Array, 'The input field => caTissue attribute mapping file(s)'],
+        [:filters, '--filters FILE[,FILE...]', Array, 'The input value => caTissue value mapping file(s)'],
+        [:defaults, '-d', '--defaults FILE[,FILE...]', Array, 'The caTissue attribute default value file(s)'],
+        [:shims, '-s', '--shims FILE[,FILE...]', Array, 'Migration customization shim file(s) to load'],
+        [:controlled_values, '-k', '--controlled_values', 'Enable controlled value lookup'],
+        [:bad, '-b', '--bad FILE', 'Write each invalid record to the given file and continue migration'],
+        [:extract, '-x', '--extract FILE', 'Call the migration target extract method to write to the given extract'],
+        [:create, '-c', '--create', 'Always create the migration target'],
+        [:unique, '-u', '--unique', 'Make the migrated objects unique for testing'],
+        [:from, '--from N', Integer, 'Starting input record'],
+        [:to, '--to N', Integer, 'Ending input record'],
       ]
-  
-      # Creates a {Migrate} command with the given standard command line specifications
-      # as well as the {SPECS} command line specifications.
+
+      # Creates a {Migrate} command with the {SPECS} command line specifications
+      # as well as the optional specifications parameter.
       #
-      # @yield [opts] optional migrator factory
-      # @yieldparam [{Symbol => Object}] the {CaTissue::Migrator#initialize} creation options
-      # @see CaRuby::Command#run
-      def initialize(&factory)
-        super(SPECS) { |opts| migrate(opts, &factory) }
+      # @param (see CaRuby::CLI::Command#initialize)
+      # @yield (see #migrate)
+      # @yieldparam (see #migrate)
+      def initialize(specs=[], &block)
+        super(specs.concat(SPECS)) { |opts| migrate(opts, &block) }
       end
   
       private
       
-      # Starts a Migrator with the command-line options.
+      # Starts a Migrator with the command-line options. Each input record is migrated to
+      # the caTissue database.
       #
-      # @yield [target] operation on the migration target
-      # @yieldparam [CaRuby::Resource] the migrated domain object 
-      # @see CaRuby::Command#run
-      def migrate(opts)
-        validate(opts)
-        migrator = block_given? ? yield(opts) : CaTissue::Migrator.new(opts)
-        migrator.migrate_to_database
+      # @param opts (see CaTissue::Migrator#initialize)
+      # @yield (see CaTissue::Migrator#migrate_to_database)
+      # @yieldparam (see CaTissue::Migrator#migrate_to_database)
+      def migrate(opts, &block)
+        opts[:target] = resolve(opts[:target])
+        # Migrate the input.
+        CaTissue::Migrator.new(opts).migrate_to_database(&block)
       end
       
-      def validate(opts)
-        tgt = opts[:target]
-        if tgt.nil? then raise ArgumentError.new("Missing required migration target class option") end
+      # Resolves the given target class name in the caTissue context.
+      #
+      # @param [String] name the target class name
+      # @return [Class] the resolved class
+      # @raise [NameError] if the class could not be resolved
+      def resolve(name)
+        return if name.nil?
         begin
-          opts[:target] = CaTissue.const_get(tgt)
-        rescue Exception
-          logger.fatal("Could not load CaTissue class #{tgt} - #{$!}.\n#{$@.qp}")
-          raise MigrationError.new("Could not load migration target class #{tgt}")
+          # Strip the CaTissue module prefix, if necessary.
+          cnm = name.sub(/^CaTissue::/, '')
+          # Resolve the class in the CaTissue context.
+          CaTissue.module_for_name(cnm)
+        rescue Exception => e
+          Jinx.fail(NameError, "Could not load migration target class #{name}", e)
         end
       end
     end

data/lib/catissue/cli/smoke.rb

@@ -1,5 +1,4 @@
-require 'catissue/cli/command'
-require 'catissue/database'
+require File.dirname(__FILE__) + '/command'
 
 module CaTissue
   module CLI
@@ -29,7 +28,7 @@ module CaTissue
         rescue Exception => e
           logger.error("caTissue database access was unsuccessful - #{e}:\n#{e.backtrace.qp}")
           puts "caTissue database access was unsuccessful - #{e}."
-          puts "See the log at #{DEF_LOG_FILE} for more information."
+          puts "See the log for more information."
         end
         
         if site then

data/lib/catissue/database/annotation/annotation_service.rb

@@ -1,7 +1,6 @@
-require 'caruby/util/inflector'
+require 'jinx/helpers/inflector'
 require 'caruby/database/sql_executor'
 require 'caruby/database/persistence_service'
-require 'catissue/annotation/annotatable'
 
 module CaTissue
   module Annotation
@@ -19,16 +18,14 @@ module CaTissue
         @intgtr = integrator
       end
 
-      # Augments the {CaRuby::PersistenceService} create method to handle caTissue annotation
+      # Augments the +CaRuby::PersistenceService+ create method to handle caTissue annotation
       # service peculiarities, e.g.:
-      # * assigns the identifier, since assignment is not done automatically as is the case with the
-      #   default application service
+      # * assigns the identifier, since assignment is not done automatically as is the case with
+      #   the default application service
       # * associate the annotation to the hook object
       # * Save all referenced annotation objects
       #
-      # This method can only be called on primary annotation objects. A _primary_ annotation
-      # is a top-level annotation which has a reference to the {Annotation#hook} which is
-      # being annotated.
+      # This method is only called on {Metadata#primary?} annotation objects.
       # 
       # @param [Annotation] annotation the annotation object to create
       # @return [Annotation] the annotation
@@ -43,14 +40,8 @@ module CaTissue
 
       # @param [Annotation] (see #create)
       def create_annotation(annotation)
-        # get the hook
-        hook = annotation.hook
-        # If no hook, then this is not a primary annotation. In that case, find a referenced
-        # primary annotation.
-        # If no hook, then this is not a primary annotation. In that case, find a referenced
-        # primary annotation.
-        if hook then
-          create_primary_annotation(annotation, hook)
+        if annotation.class.primary? then
+          create_primary_annotation(annotation, annotation.hook)
         else
           create_nonprimary_annotation(annotation)
         end
@@ -101,4 +92,4 @@ module CaTissue
       end
     end
   end
-end
+end

data/lib/catissue/database/annotation/entity_facade.rb

@@ -1,12 +1,14 @@
 require 'singleton'
-require 'caruby/import/java'
+require 'jinx/import/java'
 require 'caruby/database/sql_executor'
 require 'catissue/database/annotation/id_generator'
 
 module CaTissue
   module Annotation
-    # EntityFacade is the caRuby substitue for the broken caTissue EntityManager. EntityManager is
-    # the caTissue singleton Winnebago object for doing lots of things with dynamic extensions.
+    # EntityFacade is the caRuby substitute for the broken caTissue EntityManager.
+    # EntityManager is the caTissue singleton Winnebago object for doing lots of
+    # things with dynamic extensions. The EntityManager defects are listed in the
+    # various Rubydoc quirks.
     class EntityFacade
       include Singleton
       
@@ -38,7 +40,7 @@ module CaTissue
         @idgen.next_identifier(table)
       end
       
-      # @quirk caTissue unlike the hook entity id lookup, the annotation entity id lookup strips the leading
+      # @quirk caTissue Unlike the hook entity id lookup, the annotation entity id lookup strips the leading
       #   package prefix from the annotation class name. caTissue DE API requires this undocumented inconsistency.
       #
       # @quirk caTissue call into caTissue to get entity id doesn't work. caRuby uses direct SQL instead.
@@ -56,23 +58,23 @@ module CaTissue
       # @param [Integer] eid the entity id to check
       # @return [Boolean] whether the entity is primary
       def primary?(eid)
-        result = @executor.execute { |dbh| dbh.select_one(IS_PRIMARY_SQL, eid) }
+        result = @executor.query(IS_PRIMARY_SQL, eid).first
         not result.nil?
       end
       
       # @param [Class] klass the {Annotatable} class
       # @return [Integer] the class entity id
       def hook_entity_id(klass)
-        result = @executor.execute { |dbh| dbh.select_one(HOOK_ENTITY_ID_SQL, klass.java_class.name) }
+        result = @executor.query(HOOK_ENTITY_ID_SQL, klass.java_class.name).first
         if result.nil? then raise AnnotationError.new("Entity id not found for static hook class #{klass.qp}") end
         eid = result[0].to_i
         logger.debug { "Static hook class #{klass.qp} has entity id #{eid}." }
         eid
       end
       
-      # @quirk caTissue call into caTissue to get entity id doesn't work for non-primary object.
-      #   Furthermore, the SQL used for the #{#annotation_entity_id} doesn't work for associated annotation
-      #   classes. Use alternative SQL instead.
+      # @quirk caTissue The call into caTissue to get entity id doesn't work for a non-primary object.
+      #   Furthermore, the SQL used for the #{#annotation_entity_id} doesn't work for associated
+      #   annotation classes. Use the {ASSN_ENTITY_ID_SQL} alternative SQL instead.
       #
       # @param [Integer] eid the referencing entity id
       # @param [String] name the association property name
@@ -91,16 +93,16 @@ module CaTissue
 
       # @quirk caTissue Annotation classes are incorrectly mapped to entity ids, which in turn are
       #   incorrectly mapped to a table name. A candidate work-around is to bypass the caTissue DE
-      #   mechanism and hit the DE Hibernate config files directly. However, the DE Hibernate mappings
-      #   are incorrect and possibly no longer used. Therefore, the table must be obtained by SQL
-      #   work-arounds.
+      #   mechanism and hit the DE Hibernate config files directly. However, the 1.1.2 DE Hibernate
+      #   mappings are incorrect and possibly no longer used. Therefore, the table must be obtained
+      #   by SQL work-arounds.
       #
       # @param [Annotation] obj the annotation object
       # @return [String] the entity table name
       # @param [Integer] the annotation entity identifier
       # @return [String] the entity table name
       def annotation_table_for_entity_id(eid)
-        result = @executor.execute { |dbh| dbh.select_one(TABLE_NAME_SQL, eid) }
+        result = @executor.query(TABLE_NAME_SQL, eid).first
         if result.nil? then raise AnnotationError.new("Table not found for annotation entity id #{eid}") end
         tbl = result[0]
         logger.debug { "Annotation entity with id #{eid} has table #{tbl}." }
@@ -110,14 +112,14 @@ module CaTissue
       # @param (see #associated_entity_id)
       # @return [Integer, nil] the parent entity id, if any
       def parent_entity_id(eid)
-        result = @executor.execute { |dbh| dbh.select_one(PARENT_ENTITY_ID_SQL, eid) }
+        result = @executor.query(PARENT_ENTITY_ID_SQL, eid).first
         result[0].to_i if result and result[0]
       end
       
       # Obtains the undocumented caTisue container id for the given primary entity id.
       #
-      # @quirk caTissue EntityManager.getContainerIdForEntitycontainer uses incorrect table
-      #   (cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=421&sid=5252d951301e598eebf3e90036da43cb).
+      # @quirk caTissue 1.1.2 EntityManager.getContainerIdForEntity uses an
+      #   incorrect table (cf. https://cabig-kc.nci.nih.gov/Biospecimen/forums/viewtopic.php?f=19&t=421&sid=5252d951301e598eebf3e90036da43cb).
       #   The standard DE API call submits the query:
       #     SELECT IDENTIFIER FROM dyextn_container WHERE ENTITY_ID = ?
       #   This results in the error:
@@ -126,14 +128,15 @@ module CaTissue
       #     SELECT IDENTIFIER FROM dyextn_container WHERE ABSTRACT_ENTITY_ID = ?
       #   The work-around is to call this SQL directly.
       #
-      # @quirk caTissue in 1.2, there are deprecated primary annotations with an entity id but no container id.
+      # @quirk caTissue 1.2 There are deprecated primary annotations with an entity id
+      #   but no container id.
       # 
       # @return [Integer] eid the primary entity id
       def container_id(eid)
-        # The following call is broken (see method doc).
+        # The following call is broken in caTissue 1.1.2 (see method doc).
         # EntityManager.instance.get_container_id_for_entity(eid)
-        # Work-around caTissue bug with direct query.
-        result = @executor.execute { |dbh| dbh.select_one(CTR_ID_SQL, eid) }
+        # Work-around this caTissue bug with a direct query.
+        result = @executor.query(CTR_ID_SQL, eid).first
         if result.nil? then
           logger.debug("Dynamic extension container id not found for annotation with entity id #{eid}")
           return
@@ -163,7 +166,7 @@ module CaTissue
         # The entity group and name.
         grp, name = split_annotation_entity_class_name(klass)
         # Dive into some obscure SQL.
-        result = @executor.execute { |dbh| dbh.select_one(ANN_ENTITY_ID_SQL, grp, name) }
+        result = @executor.query(ANN_ENTITY_ID_SQL, grp, name).first
         result[0].to_i if result
       end
       
@@ -208,23 +211,23 @@ module CaTissue
       end
       
       # @param (see #recursive_associated_entity_id)
-      # @return @return [Integer, nil] the directly associated entity id, if any
+      # @return [Integer, nil] the directly associated entity id, if any
       def nonrecursive_associated_entity_id(eid, role)
         logger.debug { "Finding entity id #{eid} #{role} associated entity id..." }
-        result = @executor.execute { |dbh| dbh.select_one(ASSN_ENTITY_ID_SQL, eid, role) }
-        # The role role can be a mutation of the property name with spaces inserted in the
-        # camel-case components, e.g. 'Additional Finding' instead of 'AdditionalFinding'.
+        result = @executor.query(ASSN_ENTITY_ID_SQL, eid, role).first
+        # The role can be a mutation of the property name with spaces inserted in the
+        # mixed-case components, e.g. 'Additional Finding' instead of 'AdditionalFinding'.
         # TODO - fix this kludge by finding out how the role relates to the property in the
         # database.
         if result.nil? and role =~ /.+[A-Z]/ then
           alt = role.gsub(/(.)([A-Z])/, '\1 \2')
           logger.debug { "Attempting to find  entity id #{eid} #{role} associated entity id using variant #{alt}..." }
-          result = @executor.execute { |dbh| dbh.select_one(ASSN_ENTITY_ID_SQL, eid, alt) }
+          result = @executor.query(ASSN_ENTITY_ID_SQL, eid, alt).first
         end
         if result.nil? and role =~ /[pP]athologic[^a]/ then
           alt = role.sub(/([pP])athologic/, '\1athological')
           logger.debug { "Attempting to find  entity id #{eid} #{role} associated entity id using variant #{alt}..." }
-          result = @executor.execute { |dbh| dbh.select_one(ASSN_ENTITY_ID_SQL, eid, alt) }
+          result = @executor.query(ASSN_ENTITY_ID_SQL, eid, alt).first
         end
         if result.nil? then logger.debug { "Entity id #{eid} is not directly associated with #{role}." } end
         result[0].to_i if result
@@ -250,9 +253,9 @@ EOS
       # The SQL to find an entity id for an annotation reference.
       ASSN_ENTITY_ID_SQL = <<EOS
       select assn.TARGET_ENTITY_ID
-      from DYEXTN_ATTRIBUTE attr, DYEXTN_ABSTRACT_ENTITY ae, DYEXTN_ASSOCIATION assn, DYEXTN_ROLE role
-      where assn.IDENTIFIER = attr.IDENTIFIER
-      and attr.ENTIY_ID = ae.id
+      from DYEXTN_ATTRIBUTE pa, DYEXTN_ABSTRACT_ENTITY ae, DYEXTN_ASSOCIATION assn, DYEXTN_ROLE role
+      where assn.IDENTIFIER = pa.IDENTIFIER
+      and pa.ENTIY_ID = ae.id
       and assn.TARGET_ROLE_ID = role.IDENTIFIER
       and ae.id = ?
       and role.name = ?