rbbt-util 5.5.12 → 5.5.13

checksums.yaml

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data/lib/rbbt/association/index.rb

@@ -20,6 +20,7 @@ module Association
                      if File.exists?(reverse_filename)
                        new = Persist.open_tokyocabinet(reverse_filename, false, serializer, TokyoCabinet::BDB)
                      else
+                       FileUtils.mkdir_p File.basename(reverse_filename) unless File.exists?(File.basename(reverse_filename))
                        new = Persist.open_tokyocabinet(reverse_filename, true, serializer, TokyoCabinet::BDB)
                        new.write
                        through do |key, value|
@@ -28,7 +29,7 @@ module Association
                        end
                        annotate(new)
                        new.key_field = key_field.split("~").values_at(1,0,2).compact * "~"
-                       new.close
+                       new.read
                      end
 
                      new.unnamed = true

data/lib/rbbt/association/item.rb

@@ -21,7 +21,7 @@ module AssociationItem
 
   property :target_entity => :array2single do
     type = reverse ? knowledge_base.source(database) : knowledge_base.target(database)
-    knowledge_base.annotate self.target, type if self.target.any?
+    knowledge_base.annotate self.target, type, database if self.target.any?
   end
 
   property :source_entity => :array2single do

data/lib/rbbt/knowledge_base.rb

@@ -17,7 +17,7 @@ class KnowledgeBase
 
   attr_accessor :namespace, :dir, :indices, :registry, :format, :databases, :entity_options
   def initialize(dir, namespace = nil)
-    @dir = Path.setup dir
+    @dir = Path.setup(dir).find
 
     @namespace = namespace
     @format = IndiferentHash.setup({})
@@ -179,15 +179,18 @@ class KnowledgeBase
 
   #{{{ Annotate
   
-  def entity_options_for(type)
+  def entity_options_for(type, database_name = nil)
     options = entity_options[Entity.formats[type]] || {}
     options[:format] = @format[type] if @format.include? :type
     options = {:organism => namespace}.merge(options)
+    if database_name and (database = get_database(database_name)).entity_options
+      options = options.merge database.entity_options
+    end
     options
   end
 
-  def annotate(entities, type)
-    Misc.prepare_entity(entities, type, entity_options_for(type))
+  def annotate(entities, type, database = nil)
+    Misc.prepare_entity(entities, type, entity_options_for(type, database))
   end
 
   #{{{ Identify

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.12
+  version: 5.5.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-03 00:00:00.000000000 Z
+date: 2013-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake