caruby-tissue 1.3.4 → 1.3.5

data/History.txt

@@ -1,28 +1,32 @@
 === 1.2.1 / 2010-11-23
 
-* Initial public release
+* Initial public release.
 
 === 1.2.2 / 2010-11-30
 
-* Enable Galena example
+* Enable Galena example.
 
 === 1.2.3 / 2011-02-18
 
-* Support Dynamic Extensions
+* Support Dynamic Extensions.
 
 === 1.3.1 / 2011-02-18
 
-* Full PCBIN DE support
+* Full PCBIN DE support.
 
 === 1.3.2 / 2011-02-25
 
-* Minor migration bug fixes
+* Minor migration bug fixes.
 
 === 1.3.3 / 2011-02-26
 
-* JRuby 1.5 upgrade
+* JRuby 1.5 upgrade.
 
 === 1.3.4 / 2011-02-26
 
-* Use caruby-core JRuby 1.5 bug work-around
+* Use caruby-core JRuby 1.5 bug work-around.
+
+=== 1.3.5 / 2011-03-04
+
+* Support annotation migration.
 

data/lib/catissue/annotation/annotatable_class.rb

@@ -13,7 +13,11 @@ module CaTissue
     def self.extended(klass)
       super
       # the annotation name => spec hash 
-      klass.class_eval { extend Forwardable; @ann_spec_hash = {} }
+      klass.class_eval do
+        extend Forwardable
+        @ann_spec_hash = {}
+        @local_ann_attrs = []
+      end
     end
     
     # @return [Integer, nil] this class's entity id, if it exists, otherwise the superclass effective entity id
@@ -79,6 +83,16 @@ module CaTissue
       end
     end
     
+    def printable_attributes
+      @prbl_attrs ||= super.union(annotation_attributes)
+    end
+    
+    def annotation_attributes
+      @ann_attrs ||= append_ancestor_enum(@local_ann_attrs) do |sc|
+        sc.annotation_attributes if sc < Annotatable
+      end
+    end
+    
     protected
     
     # @return [<AnnotationModule>] the annotation modules in the class hierarchy
@@ -250,6 +264,9 @@ module CaTissue
       
       # the annotation is a dependent
       add_dependent_attribute(attribute, :logical)
+      
+      # add the attribute to the local collection
+      @local_ann_attrs << attribute
     end
   end
 end

data/lib/catissue/annotation/annotation.rb

@@ -31,6 +31,11 @@ module CaTissue
     
     # If there is no conventional owner, then try the hook.
     #
+    # caTissue alert - DE annotations have a physical dependency ownership model that is at odds
+    # with the logical model. An annotation does not directly reference its static hook owner
+    # instance. Rather, it references the hook proxy which stands in for the hook entity in the
+    # annotation package. 
+    #
     # @return the {CaRuby::Resource#owner} or the {#hook}
     def owner
       super or hook

data/lib/catissue/annotation/annotation_class.rb

@@ -49,6 +49,16 @@ module CaTissue
       dependent_attributes.each { |attr| save_dependent_attribute(annotation, attr) }
     end
     
+    # @return [Boolean] whether this annotation refers to a {#primary?} annotation
+    def secondary?
+      not @proxy_attribute.nil?
+    end
+    
+    # @return [Boolean] whether this annotation is neither a {#primary?} nor a #{secondary} annotation
+    def tertiary_annotation
+      not (primary? or secondary?)
+    end
+    
     # Detects or creates the proxy attribute that references the given proxy class.
     # if this is a primary_entity annotation class which does not
     # have a caTissue proxy property.
@@ -62,7 +72,9 @@ module CaTissue
       # set the hook
       self.hook = proxy.hook
       # primary superclass gets a proxy as well
-      if superclass < Annotation and superclass.primary? then superclass.proxy = proxy end
+      if superclass < Annotation then
+        superclass.ensure_primary_has_proxy(proxy)
+      end
     end
     
     # @param [Class] klass the hook class for this primary annotation
@@ -184,7 +196,7 @@ module CaTissue
     
     def obtain_proxy_attribute(proxy)
       # parent proxy is reserved for RadiationTherapy use case described in ParticipantTest.
-      # TODO - either support this use case of delete the parent proxy call
+      # TODO - either support this use case or delete the parent proxy call
       detect_proxy_attribute(proxy) or create_proxy_attribute(proxy) or parent_proxy_attribute
     end
     
@@ -213,7 +225,7 @@ module CaTissue
     def create_proxy_attribute(proxy)
       # the proxy attribute symbol
       attr = proxy.name.demodulize.underscore.to_sym
-      logger.debug { "Creating primary annotation #{qp} proxy attribute #{attr}..." }
+      logger.debug { "Creating primary annotation #{qp} proxy #{proxy} attribute #{attr}..." }
       # make the attribute
       attr_accessor(attr)
       # Add the attribute. Setting the saved flag ensures that the save template passed to

data/lib/catissue/annotation/proxy_class.rb

@@ -37,10 +37,11 @@ module CaTissue
       
       # Adds each proxy => annotation reference as a dependent attribute.
       def add_annotation_dependents
+        # first add the direct dependents
         annotation_attributes.each_metadata do |attr_md|
           attr_md.type.add_dependent_attributes
-          attr_md.type.proxy = self
         end
+        # now add the recursive indirect dependents
         annotation_attributes.each_metadata do |attr_md|
           attr_md.type.add_dependent_attribute_closure
         end

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

@@ -37,21 +37,28 @@ module CaTissue
       # @return [Annotation] the annotation
       def create(annotation)
         logger.debug { "Creating annotation #{annotation.qp}..." }
-        # get the hook
+        time { create_annotation(annotation) }
+        logger.debug { "Created annotation #{annotation}." }
+        annotation
+      end
+      
+      private
+
+      # @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
-          time { create_primary_annotation(annotation, hook) }
+          create_primary_annotation(annotation, hook)
         else
           create_secondary_annotation(annotation)
         end
-        logger.debug { "Created annotation #{annotation}." }
-        annotation
       end
       
-      private
-      
       # @param annotation (see #create)
       # @param [Annotable] the annotatable object referenced by this annotation
       def create_primary_annotation(annotation, hook)

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

@@ -19,7 +19,9 @@ module CaTissue
     # @param [String] name the service name
     # @return [Annotation::AnnotationService] the annotation service
     def create_annotation_service(name)
-      Annotation::AnnotationService.new(@database, name, :integration_service => @integration_service)
+      host = CaTissue.access_properties[:host]
+      port = CaTissue.access_properties[:port]
+      Annotation::AnnotationService.new(@database, name, :host => host, :port => port, :integration_service => @integration_service)
     end
   end
 end

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

@@ -5,25 +5,16 @@ require 'catissue/database/annotation/id_generator'
 
 module CaTissue
   module Annotation
-    # Import this EntityManager dependency before EntityManager.
-    java_import('edu.wustl.common.security.exceptions.UserNotAuthorizedException')
-    
-    # Import the caTissue Java EntityManager.
-    java_import('edu.common.dynamicextensions.entitymanager.EntityManager')
-   
-    # EntityFacade is the caRuby interface to the caTissue EntityManager. EntityManager is
+    # 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.
     class EntityFacade
       include Singleton
       
       private
       
-      # Initializes the caTissue EntityManager, an id generator and a SQL executor. The id
-      # generator and executor are used for the caTissue bug work-arounds described in the
-      # method docs and {IdGenerator}.
+      # Initializes the id generator and a SQL executor. The id generator and executor are
+      # used for the caTissue bug work-arounds described in the method docs and {IdGenerator}.
       def initialize
-        # the encapsulated caTissue singleton
-        @emgr = EntityManager.instance
         # the work-around id generator
         @idgen = IdGenerator.new
         # a general-purpose SQL executor for calling the work-arounds
@@ -72,7 +63,11 @@ module CaTissue
       # @param [Class] klass the {Annotatable} class
       # @return [Integer] the class entity id
       def hook_entity_id(klass)
-        entity_id_for_class_designator(klass.java_class.name)
+        result = @executor.execute { |dbh| dbh.select_one(HOOK_ENTITY_ID_SQL, klass.java_class.name) }
+        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
       
       # caTissue alert - call into caTissue to get entity id doesn't work for non-primary object.
@@ -116,7 +111,7 @@ module CaTissue
       # @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[0] if result
+        result[0].to_i if result and result[0]
       end
       
       # Obtains the undocumented caTisue container id for the given primary entity id.
@@ -138,10 +133,10 @@ module CaTissue
         # 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) }
-        cid = result[0].to_i if result
-        if cid.nil? then
+        if result.nil? then
           raise AnnotationError.new("Dynamic extension container id not found for annotation #{annotation} with entity id #{eid}")
         end
+        cid = result[0].to_i
         logger.debug { "Annotation with entity id #{eid} has container id #{cid}." }
         cid
       end
@@ -163,7 +158,7 @@ module CaTissue
         pkg, cls_nm = klass.java_class.name.split('.')
         # Dive into some obscure SQL
         result = @executor.execute { |dbh| dbh.select_one(CTR_ENTITY_ID_SQL, pkg, cls_nm) }
-        result[0] if result
+        result[0].to_i if result
       end
       
       # @param (see #primary_entity_id)
@@ -213,20 +208,17 @@ module CaTissue
           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) }
         end
-        if result.nil? then
-          logger.debug { "Entity id #{eid} is not directly associated with #{role}." }
-        end
-        result[0] if result
-      end
-      
-      # @param [String] designator the class name, demodulized in the case of an annotation entity
-      # @return [Integer] the caTissue entity id for the given class name
-      # @raise [CaRuby::DatabaseError] if the DE entity id is not found for the given designator
-      def entity_id_for_class_designator(designator)
-        @emgr.getEntityId(designator) or
-          raise CaRuby::DatabaseError.new("Dynamic extension entity id not found for #{designator}")
+        if result.nil? then logger.debug { "Entity id #{eid} is not directly associated with #{role}." } end
+        result[0].to_i if result
       end
       
+      # The SQL to find an entity id for a primary entity.
+      HOOK_ENTITY_ID_SQL = <<EOS
+      select IDENTIFIER
+      from DYEXTN_ABSTRACT_METADATA
+      where NAME = ?
+EOS
+     
       # The SQL to find an entity id for a primary entity.
       CTR_ENTITY_ID_SQL = <<EOS
       select ctr.ABSTRACT_ENTITY_ID

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

@@ -6,15 +6,17 @@ module CaTissue
     class IntegrationService < CaRuby::PersistenceService
       SERVICE_NAME = 'deintegration'
 
-      java_import('deintegration.EntityMap')
+      java_import 'deintegration.EntityMap'
       
-      java_import('deintegration.EntityMapRecord')
+      java_import 'deintegration.EntityMapRecord'
       
-      java_import('deintegration.FormContext')
+      java_import 'deintegration.FormContext'
 
       # @param [EntityFacade] the global entity manager
       def initialize
-        super(SERVICE_NAME)
+      host = CaTissue.access_properties[:host]
+      port = CaTissue.access_properties[:port]
+        super(SERVICE_NAME, :host => host, :port => port)
         # SQL executor to handle caTissue DE API bug work-around 
         @executor = CaRuby::SQLExecutor.new(CaTissue.access_properties)
       end

data/lib/catissue/database.rb

@@ -313,7 +313,7 @@ module CaTissue
         end
         logger.debug { "Work around caTissue Bug #164 by setting the #{obj.qp} update template #{template.qp} external_identifiers to nil." }
         template.external_identifiers = nil
-      elsif Annotation === obj and obj.class.proxy_attribute then
+      elsif Annotation === obj and obj.class.secondary? then
         copy_annotation_proxy_owner_to_template(obj, template)
       end
       super
@@ -395,7 +395,7 @@ module CaTissue
       specimen.is_available = true
       oiqty = specimen.initial_quantity
       oaqty = specimen.available_quantity
-      ostatus =  specimen.activity_status
+      ostatus = specimen.activity_status
       specimen.initial_quantity = 1.0
       specimen.available_quantity = 1.0
       specimen.activity_status = 'Active'

data/lib/catissue/domain/abstract_domain_object.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # explicitly import AbstractDomainObject, since it is not in the default CaTissue package and therefore can't be auto-imported
-  java_import('edu.wustl.common.domain.AbstractDomainObject')
+  java_import Java::edu.wustl.common.domain.AbstractDomainObject
 
   class AbstractDomainObject
     include Resource

data/lib/catissue/domain/abstract_position.rb

@@ -1,7 +1,7 @@
 require 'catissue/util/position'
 
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.AbstractPosition')
+  java_import Java::edu.wustl.catissuecore.domain.AbstractPosition
 
   # The +caTissue+ AbstractPosition class is augmented with a comparison operator and the
   # zero-based +row+ and +column+ methods wrapping the corresponding one-based dimension

data/lib/catissue/domain/abstract_specimen.rb

@@ -2,7 +2,7 @@ require 'set'
 require 'caruby/util/inflector'
 
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.AbstractSpecimen')
+  java_import Java::edu.wustl.catissuecore.domain.AbstractSpecimen
 
   class AbstractSpecimen
     include Resource

data/lib/catissue/domain/abstract_specimen_collection_group.rb

@@ -1,5 +1,5 @@
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.AbstractSpecimenCollectionGroup')
+  java_import Java::edu.wustl.catissuecore.domain.AbstractSpecimenCollectionGroup
 
   class AbstractSpecimenCollectionGroup
     include Resource

data/lib/catissue/domain/address.rb

@@ -1,5 +1,5 @@
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.Address')
+  java_import Java::edu.wustl.catissuecore.domain.Address
 
   class Address
     include Resource

data/lib/catissue/domain/cancer_research_group.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CancerResearchGroup')
+  java_import Java::edu.wustl.catissuecore.domain.CancerResearchGroup
 
   # The CancerResearchGroup domain class.
   class CancerResearchGroup

data/lib/catissue/domain/capacity.rb

@@ -1,7 +1,7 @@
 require 'caruby/util/coordinate'
 
 module CaTissue
-  java_import('edu.wustl.catissuecore.domain.Capacity')
+  java_import Java::edu.wustl.catissuecore.domain.Capacity
 
   class Capacity
     include Resource

data/lib/catissue/domain/check_in_check_out_event_parameter.rb

@@ -1,6 +1,6 @@
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CheckInCheckOutEventParameter')
+  java_import Java::edu.wustl.catissuecore.domain.CheckInCheckOutEventParameter
 
   class CheckInCheckOutEventParameter
     include Resource

data/lib/catissue/domain/collection_event_parameters.rb

@@ -2,7 +2,7 @@ require 'catissue/domain/scg_event_parameters'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CollectionEventParameters')
+  java_import Java::edu.wustl.catissuecore.domain.CollectionEventParameters
 
   class CollectionEventParameters
     include Resource, SCGEventParameters

data/lib/catissue/domain/collection_protocol.rb

@@ -3,7 +3,7 @@ require 'catissue/domain/hash_code'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CollectionProtocol')
+  java_import Java::edu.wustl.catissuecore.domain.CollectionProtocol
 
   # The CollectionProtocol domain class.
   class CollectionProtocol

data/lib/catissue/domain/collection_protocol_event.rb

@@ -3,7 +3,7 @@ require 'catissue/domain/hash_code'
 
 module CaTissue
   # import the Java class
-  java_import('edu.wustl.catissuecore.domain.CollectionProtocolEvent')
+  java_import Java::edu.wustl.catissuecore.domain.CollectionProtocolEvent
 
   # The CollectionProtocolRegistration domain class.
   class CollectionProtocolEvent