rbbt-entities 2.0.0 → 2.1.0

data/lib/rbbt/entity.rb

@@ -1,6 +1,7 @@
 require 'rbbt/annotations'
 
-module Entity
+module Entity 
+
   class << self
     attr_accessor :formats, :entity_property_cache, :entity_list_cache
   end
@@ -12,33 +13,20 @@ module Entity
   UNPERSISTED_PREFIX = "entity_unpersisted_property_"
 
   def self.extended(base)
-    base.extend Annotation unless Annotation === base
-
-
+    base.extend Annotation
     Entity.formats[base.to_s] = base
+
     base.module_eval do
       attr_accessor :_ary_property_cache
 
+      def _ary_property_cache
+        @_ary_property_cache ||= {}
+      end
+
       if not methods.include? "prev_entity_extended"
         class << self
           attr_accessor :template, :list_template, :action_template, :list_action_template, :keep_id
-          alias prev_entity_extended extended 
         end 
-
-        def self.extended(data)
-          prev_entity_extended(data)
-
-          data._ary_property_cache = {}
-
-          if Array === data and 
-            not AnnotatedArray === data and 
-            not (data.compact.first != nil and Annotated === data.compact.first and (data.annotation_types - data.compact.first.annotation_types).any?)
-
-            data.extend AnnotatedArray
-          end
-
-          data
-        end
       end
 
       def self.format=(formats)
@@ -69,7 +57,7 @@ module Entity
         end
       end
 
-      def clean_annotations
+      def clean_annotations_new
         case
         when self.nil?
           nil
@@ -143,7 +131,7 @@ module Entity
             case
             when Array === self
               self.send(ary_name, *args)
-            when (Array === self.container and self.container.respond_to? ary_name)
+            when (Array === self.container and not self.container_index.nil? and self.container.respond_to? ary_name)
               cache_code = Misc.hash2md5({:name => ary_name, :args => args})
               res = (self.container._ary_property_cache[cache_code] ||=  self.container.send(name, *args))
               if Hash === res

data/lib/rbbt/entity/genomic_mutation.rb

@@ -34,12 +34,16 @@ module GenomicMutation
   #persist :guess_watson
 
   def watson
-    if @watson.nil? and Array === self
-      @watson = :missing
-      @watson = guess_watson
+    if @current_watson.nil?
+      current = annotation_values[:watson]
+      if current.nil? and Array === self
+        watson = current = guess_watson
+      else
+        current
+      end
+      @current_watson = current
     end
-    @watson = false if @watson == "false"
-    @watson
+    @current_watson
   end
 
   def orig_watson
@@ -274,16 +278,21 @@ module GenomicMutation
     genes = nil
     genes = genes_tsv.chunked_values_at self
     Gene.setup(genes, "Ensembl Gene ID", organism)
+    genes
   end
   #persist :_ary_genes
 
   property :affected_genes => :array2single do
     _mutated_isoforms = mutated_isoforms
+
     mi_gene = Misc.process_to_hash(MutatedIsoform.setup(_mutated_isoforms.compact.flatten.uniq, organism)){|mis| mis.protein.gene}
-    from_protein = mutated_isoforms.collect{|mis|
+
+    _mutated_isoforms = _mutated_isoforms.clean_annotations if _mutated_isoforms.respond_to? :clean_annotations
+    from_protein = _mutated_isoforms.collect{|mis|
       genes = mis.nil? ? [] : mi_gene.values_at(*mis).compact
       Gene.setup(genes.uniq, "Ensembl Gene ID", organism)
     }
+
     is_exon_junction = self.in_exon_junction?.zip(self.type).collect{|in_ex,type| in_ex and type != "none"}
     genes_with_altered_splicing = self.transcripts_with_affected_splicing.collect{|transcripts| transcripts.gene}
     from_protein.each_with_index do |list, i|
@@ -292,11 +301,11 @@ module GenomicMutation
         list.uniq!
       end
     end
+
     Gene.setup(from_protein, "Ensembl Gene ID", organism)
   end
   #persist :_ary_affected_genes
 
-
   property :relevant? => :array2single do
     affected_genes.collect{|list| list and list.any?}
   end
@@ -327,7 +336,10 @@ module GenomicMutation
   property :mutated_isoforms => :array2single do
     res = Sequence.job(:mutated_isoforms_for_genomic_mutations, jobname, :watson => watson, :organism => organism, :mutations => self.clean_annotations).run.chunked_values_at self
     res.each{|list| list.organism = organism unless list.nil?}
-    res.compact[0].annotate res if res.compact[0].respond_to? :annotate
+    if Annotated === (first = res.compact[0])
+      first.annotate(res)
+      res.extend AnnotatedArray
+    end
     res
   end
   #persist :_ary_mutated_isoforms
@@ -468,6 +480,7 @@ module GenomicMutation
   end
 
   property :damaging? => :array2single do |*args|
+
     all_mutated_isoforms = mutated_isoforms.compact.flatten
     damaged_mutated_isoforms = all_mutated_isoforms.select{|mi| mi.damaged?(*args)}
     exon_junctions.zip(mutated_isoforms, self.type).collect do |exs, mis, type|
@@ -475,7 +488,6 @@ module GenomicMutation
       (Array === mis and (damaged_mutated_isoforms & mis).any?)
     end
   end
-  #persist :damaging?
 
   property :worst_consequence => :array2single do |*args|
     gene = args.first

data/lib/rbbt/entity/genotype.rb

@@ -63,7 +63,7 @@ module Genotype
 
     def metagenotype
       organism = self.collect{|g| g.organism}.compact.first
-      orig_watson = self.collect{|g| g.orig_watson}.compact.first
+      orig_watson = self.collect{|g| g.watson}.compact.first
       GenomicMutation.setup(self.dup.flatten, jobname, organism, orig_watson).extend Genotype
     end
 

data/lib/rbbt/entity/transcript.rb

@@ -16,7 +16,11 @@ module Transcript
           else
             @@enst2ensg[organism][transcript]
           end
-    Gene.setup(res, "Ensembl Gene ID", organism) if defined? Gene
+
+    if defined? Gene
+      Gene.fast_setup(res, {:format => "Ensembl Gene ID", :organism => organism})
+    end
+
     res
   end
 

data/test/rbbt/entity/test_genomic_mutation.rb

@@ -74,7 +74,14 @@ class TestGenomicMutation < Test::Unit::TestCase
     assert(SPLICING2.transcripts_with_affected_splicing.empty?)
   end
 
+  def test_genes_persist
 
+    GenomicMutation.with_persisted :genes do
+
+      m = MUTATION.annotate(MUTATION.dup)
+      assert AnnotatedArray === m.genes
+    end
+  end
 end
 
 

data/test/rbbt/test_entity.rb

@@ -4,9 +4,19 @@ require 'rbbt/entity'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
+class TestA
+  attr_accessor :foo, :bar
+  def initialize(foo, bar)
+    @foo = foo
+    @bar = bar
+  end
+end
+
 module ReversableString
   extend Entity
-  
+
+  self.annotation :foo, :bar
+
   property :reverse_text_ary => :array do
     $count += 1
     self.collect{|s| s.reverse}
@@ -54,9 +64,9 @@ end
 
 class TestEntity < Test::Unit::TestCase
 
-  def _test_property_ary
+  def test_property_ary
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup(a)
 
     $count = 0
 
@@ -74,9 +84,9 @@ class TestEntity < Test::Unit::TestCase
     end
   end
 
-  def _test_property_single
+  def test_property_single
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup a
 
     $count = 0
 
@@ -86,9 +96,9 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 3, $count
   end
 
-  def _test_property_ary_p
+  def test_property_ary_p
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup a
 
     $count = 0
 
@@ -97,9 +107,9 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 1, $count
   end
 
-  def _test_property_single_p
+  def test_property_single_p
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup a
 
     $count = 0
 
@@ -109,9 +119,9 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 2, $count
   end
 
-  def _test_property_ary_p_array
+  def test_property_ary_p_array
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup a
 
     $count = 0
 
@@ -121,9 +131,9 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 1, $count
   end
 
-  def _test_unpersist
+  def test_unpersist
     a = ["String1", "String2"]
-    a.extend ReversableString
+    ReversableString.setup a
 
     # Before persist
     assert(! ReversableString.persisted?(:random))
@@ -150,7 +160,7 @@ class TestEntity < Test::Unit::TestCase
 
   end
 
-  def _test_persist_annotations
+  def test_persist_annotations
     string = 'aaabbbccc'
     ReversableString.setup(string)
     assert_equal string.length, string.annotation_list.length
@@ -158,14 +168,25 @@ class TestEntity < Test::Unit::TestCase
   end
 
   def __test_performance
+    require 'rbbt/entity/gene'
+    Misc.profile(:min_percent => 2) do
+      1000.times do
+        TestA.new "foo", "bar"
+      end
+    end
 
-    require 'rbbt/workflow'
-    Workflow.require_workflow "StudyExplorer"
+    Misc.profile(:min_percent => 2) do
+      1000.times do
+        Gene.setup_positional("", "foo", "bar")
+      end
+    end
 
-    s = Study.setup("CLL")
-    mutations = s.cohort.metagenotype
-    Misc.profile_html(:min_percent => 1) do
-      mutated_isoforms = mutations.each{|m| m.genes.each{|g| g}}
+    Misc.benchmark(100000) do
+      Gene.setup("", :foo => "foo", :bar => "bar")
+    end
+
+    Misc.benchmark(100000) do
+      TestA.new "foo", "bar"
     end
   end
 
@@ -174,14 +195,21 @@ class TestEntity < Test::Unit::TestCase
     Workflow.require_workflow "StudyExplorer"
 
     s = Study.setup("CLL")
-    mutations = s.cohort.metagenotype.mutated_isoforms
+    mutations = s.cohort.metagenotype
+
+    mis = mutations.mutated_isoforms.compact.flatten
+
+    Misc.profile(:min_percent => 1) do
+      mis.each{|m| m}
+    end
+
 
-    Misc.benchmark(100) do
-      mutations.each{|m| m}
+    Misc.benchmark(10) do
+      mis.each{|m| m}
     end
 
-    Misc.benchmark(100) do
-      mutations.clean_annotations.each{|m| m}
+    Misc.benchmark(10) do
+      mis.clean_annotations.each{|m| m}
     end
 
     m = mutations.first

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-entities
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2013-01-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -65,13 +65,13 @@ files:
 - lib/rbbt/entity/pmid.rb
 - lib/rbbt/entity/protein.rb
 - lib/rbbt/entity/transcript.rb
-- test/test_helper.rb
-- test/rbbt/entity/test_gene.rb
-- test/rbbt/entity/test_genomic_mutation.rb
-- test/rbbt/entity/test_mutated_isoform.rb
+- test/rbbt/test_entity.rb
 - test/rbbt/entity/test_protein.rb
+- test/rbbt/entity/test_mutated_isoform.rb
 - test/rbbt/entity/test_pmid.rb
-- test/rbbt/test_entity.rb
+- test/rbbt/entity/test_gene.rb
+- test/rbbt/entity/test_genomic_mutation.rb
+- test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
 post_install_message: 
@@ -97,10 +97,10 @@ signing_key:
 specification_version: 3
 summary: Entities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/entity/test_gene.rb
-- test/rbbt/entity/test_genomic_mutation.rb
-- test/rbbt/entity/test_mutated_isoform.rb
+- test/rbbt/test_entity.rb
 - test/rbbt/entity/test_protein.rb
+- test/rbbt/entity/test_mutated_isoform.rb
 - test/rbbt/entity/test_pmid.rb
-- test/rbbt/test_entity.rb
+- test/rbbt/entity/test_gene.rb
+- test/rbbt/entity/test_genomic_mutation.rb
+- test/test_helper.rb