rbbt-util 5.14.35 → 5.14.36

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: b4e41917f06c7d28736b6ed235c61271eb25ec47
+  metadata.gz: 795e7afaaeccea346ef27ef5a13ccc114072207e
+  data.tar.gz: e8cb3fd1d85d3c30d2970ec75f63d8ce408f471d
 SHA512:
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-  data.tar.gz: e9432f28095748fd4d25e945d1a9cb4c2b100708e200216ee589a9f57eb19d999d55ac3556ae040a388775faba145212da99ff3ffbe0001cc218821ffbf53597
+  metadata.gz: 94cac0c82c60c0759be8bf32296b016666b2408751eab32d32b7b2e97e059374c3ff33ed427ac05b696169e8ce71c15839a4eedd7a7573ae7bc0add452a257e8
+  data.tar.gz: f7e41b218c3809e5048fbf94121e93192c28a1ab11e1c9c423d8bb0d585d3aea62e72d371e09f9421a58d4fe42f8c3f21a482a146ae198fb2edc84413fda567c

data/lib/rbbt/association/database.rb

@@ -71,6 +71,7 @@ module Association
     info_fields = field_pos.collect{|f| f == :key ? :key : all_fields[f]}
     options = options.merge({:key_field => source_field, :fields =>  info_fields})
 
+
     tsv = tsv.reorder source_field, fields if true or source_field != tsv.key_field or (fields and tsv.fields != fields)
 
     tsv.key_field = source_header
@@ -136,16 +137,20 @@ module Association
   end
 
   def self.database(file,  options = {})
-    case file
-    when TSV
-      file = file.to_double unless file.type == :double
-      reorder_tsv(file, options.dup)
-    when IO
-      open_stream(file, options.dup)
-    else
-      stream = TSV.get_stream(file)
-      open_stream(stream, options.dup)
-    end
+    database = case file
+               when TSV
+                 file = file.to_double unless file.type == :double
+                 reorder_tsv(file, options.dup)
+               when IO
+                 open_stream(file, options.dup)
+               else
+                 stream = TSV.get_stream(file)
+                 open_stream(stream, options.dup)
+               end
+
+    database.entity_options = options[:entity_options] if options[:entity_options]
+
+    database
   end
   
 end

data/lib/rbbt/association/index.rb

@@ -1,5 +1,6 @@
 require 'rbbt/tsv'
 require 'rbbt/association/open'
+require 'rbbt/association/item'
 
 module Association
   def self.index(file, options = nil, persist_options = nil)
@@ -16,13 +17,16 @@ module Association
       undirected = options[:undirected]
 
       persist_options[:file] = persist_options[:file] + '.database' if persist_options[:file]
+
       database = open(file, options, persist_options.dup.merge(:engine => "HDB"))
 
-      undirected = true if undirected.nil? and database.key_field == database.fields.first
+      source_field = database.key_field
 
       fields = database.fields
-      source_field = database.key_field
       target_field = fields.first.split(":").last
+
+      undirected = true if undirected.nil? and source_field == target_field
+
       key_field = [source_field, target_field, undirected ? "undirected" : nil].compact * "~"
 
       TSV.setup(data, :key_field => key_field, :fields => fields[1..-1], :type => :list, :serializer => :list)
@@ -33,46 +37,48 @@ module Association
       data.serializer = :list 
 
       database.with_unnamed do
-        database.through do |source, values|
-          case database.type
-          when :single
-            values = [[values]]
-          when :list
-            values = values.collect{|v| [v] }
-          when :flat
-            values = [values]
-          end
-          next if values.empty?
-          next if source.nil? or source.empty?
-          next if values.empty?
-
-          targets, *rest = values
-
-          size = targets ? targets.length : 0
-
-          rest.each_with_index do |list,i|
-            list.replace [list.first] * size if list.length == 1
-          end if recycle and size > 1
-
-          rest = Misc.zip_fields rest
-
-          annotations = rest.length > 1 ?
-            targets.zip(rest) :
-            targets.zip(rest * targets.length) 
-
-          annotations.each do |target, info|
-            next if target.nil? or target.empty?
-            key = [source, target] * "~"
-            if data[key].nil? or info.nil?
-              data[key] = info
-            else
-              old_info = data[key]
-              info = old_info.zip(info).collect{|p| p * ";;" }
-              data[key] = info
+        database.with_monitor(options[:monitor]) do
+          database.through do |source, values|
+            case database.type
+            when :single
+              values = [[values]]
+            when :list
+              values = values.collect{|v| [v] }
+            when :flat
+              values = [values]
             end
-            if undirected
-              reverse_key = [target,source] * "~"
-              data[reverse_key] = info unless data.include? reverse_key
+            next if values.empty?
+            next if source.nil? or source.empty?
+            next if values.empty?
+
+            targets, *rest = values
+
+            size = targets ? targets.length : 0
+
+            rest.each_with_index do |list,i|
+              list.replace [list.first] * size if list.length == 1
+            end if recycle and size > 1
+
+            rest = Misc.zip_fields rest
+
+            annotations = rest.length > 1 ?
+              targets.zip(rest) :
+              targets.zip(rest * targets.length) 
+
+            annotations.each do |target, info|
+              next if target.nil? or target.empty?
+              key = [source, target] * "~"
+              if data[key].nil? or info.nil?
+                data[key] = info
+              else
+                old_info = data[key]
+                info = old_info.zip(info).collect{|p| p * ";;" }
+                data[key] = info
+              end
+              if undirected
+                reverse_key = [target,source] * "~"
+                data[reverse_key] = info unless data.include? reverse_key
+              end
             end
           end
         end
@@ -83,9 +89,11 @@ module Association
     end.tap do |data|
       data.read if not Hash === data and data.respond_to? :read
       Association::Index.setup data
+      data.entity_options = options[:entity_options] if options[:entity_options]
       data
     end
   end
+
   module Index
 
     attr_accessor :source_field, :target_field, :undirected
@@ -156,6 +164,26 @@ module Association
       end
     end
 
+    def to_matrix(value_field = nil, &block)
+      value_field = fields.first if value_field.nil? and fields.length == 1
+      value_pos = identify_field value_field if value_field and String === value_field
+      key_field = source_field
+
+      tsv = if value_pos
+              AssociationItem.incidence self.keys, key_field do |key|
+                if block_given? 
+                  yield self[key][value_pos]
+                else
+                  self[key][value_pos]
+                end
+              end
+            elsif block_given?
+              AssociationItem.incidence self.keys, key_field, &block
+            else
+              AssociationItem.incidence self.keys, key_field 
+            end
+    end
+
     #{{{ Subset
 
     def subset(source, target)

data/lib/rbbt/association/item.rb

@@ -54,23 +54,27 @@ module AssociationItem
     reverse ? knowledge_base.target(database) : knowledge_base.source(database)
   end
 
+  property :undirected => :both do
+    knowledge_base.undirected(database)
+  end
+
   property :target_entity => :array2single do
     type = reverse ? knowledge_base.source(database) : knowledge_base.target(database)
     knowledge_base.annotate self.target, type, database #if self.target.any?
   end
 
-  property :undirected => :both do
-    knowledge_base.undirected(database)
-  end
-
   property :source_entity => :array2single do
     type = reverse ? knowledge_base.target(database) : knowledge_base.source(database)
-    knowledge_base.annotate self.source, type #if self.source.any?
+    knowledge_base.annotate self.source, type, database #if self.source.any?
   end
 
+  property :index => :both do |database|
+    @index ||= knowledge_base.get_index(database)
+  end
   property :value => :array2single do
-    value = (reverse ? knowledge_base.get_index(database).reverse : knowledge_base.get_index(database)).chunked_values_at self
-    value.collect{|v| NamedArray.setup(v, knowledge_base.get_index(database).fields)}
+    index = index(database)
+    value = (reverse ? index.reverse : index).chunked_values_at self
+    value.collect{|v| NamedArray.setup(v, index.fields)}
   end
 
   property :info_fields => :both do
@@ -126,7 +130,7 @@ module AssociationItem
         value = block.call p
         matches[s][t] = value unless value.nil? or (mv = matches[s][t] and value > mv)
       else
-        matches[s] ||= Hash.new{true}
+        matches[s] ||= Hash.new{false}
         matches[s][t] ||= true 
       end
     end

data/lib/rbbt/association/open.rb

@@ -21,17 +21,20 @@ module Association
     data = Persist.persist_tsv(file, "Association Database", options, persist_options) do |data|
       tsv = Association.database(file, options.merge(:persist => persist))
       tsv = tsv.to_double unless tsv.type == :double
+
       tsv.annotate data
 
       data.serializer = :double if data.respond_to? :serializer
-      tsv.each do |k,v|
-        data[k] = v
+      tsv.with_monitor(options[:monitor]) do
+        tsv.through do |k,v|
+          data[k] = v
+        end
       end
 
-
       data
     end
-      data
+    data.entity_options = options[:entity_options] if options[:entity_options]
+    data
   end
   
 end

data/lib/rbbt/association/util.rb

@@ -116,7 +116,7 @@ module Association
       field_headers << header
     end
 
-    field_pos = info_fields.collect{|f| raise "Field #{f} not found. Options: #{info_fields* ", "}" unless all_fields.include?(f); f == :key ? 0 : all_fields.index(f);  }
+    field_pos = info_fields.collect{|f| raise "Field #{f} not found. Options: #{all_fields * ", "}" unless all_fields.include?(f); f == :key ? 0 : all_fields.index(f);  }
 
     source_format = specs[:source][2]
     target_format = specs[:target][2]

data/lib/rbbt/entity.rb

@@ -2,15 +2,19 @@ require 'rbbt/annotations'
 require 'rbbt/entity/identifiers'
 
 module Entity 
+  
+  UNPERSISTED_PREFIX = "entity_unpersisted_property_"
 
   class << self
     attr_accessor :formats, :entity_property_cache
   end
-
-  self.entity_property_cache = "var/entity_property"
   self.formats = {}
-  
-  UNPERSISTED_PREFIX = "entity_unpersisted_property_"
+  dir = (defined?(Rbbt)? Rbbt.var.entity_property : 'var/entity_property')
+  self.entity_property_cache = dir
+
+  def self.entity_property_cache=(dir)
+    @entity_property_cache = dir
+  end
 
   attr_accessor :all_formats
   def self.extended(base)
@@ -22,19 +26,19 @@ module Entity
 
       attr_accessor :template, :list_template, :action_template, :list_action_template, :keep_id
 
-      def _ary_property_cache
-        @_ary_property_cache ||= {}
-      end
-
       def self.format=(formats)
         formats = [formats] unless Array === formats
         self.all_formats ||= []
         self.all_formats = self.all_formats.concat(formats).uniq
         formats.each do |format|
-          Entity.formats[format] = self
+          Entity.formats[format] ||= self
         end
       end
 
+      def _ary_property_cache
+        @_ary_property_cache ||= {}
+      end
+
       def base_entity
         self.annotation_types.select{|m| Entity === m}.last
       end
@@ -90,7 +94,7 @@ module Entity
           define_method single_name, &block 
           define_method name do |*args|
             if Array === self
-              self.collect{|e| e.send(name, *args)}
+              self.collect{|e| e.send(single_name, *args)}
             else
               self.send(single_name, *args)
             end

data/lib/rbbt/entity/identifiers.rb

@@ -1,5 +1,4 @@
 module Entity
-
   def self.identifier_files(field)
     entity_type = Entity.formats[field]
     return [] unless entity_type and entity_type.include? Entity::Identified 
@@ -12,6 +11,12 @@ module Entity
       base.annotation :format
       base.annotation :organism
 
+
+
+      class << base
+        attr_accessor :identifier_files, :formats, :default_format, :name_format, :description_format
+      end
+
       base.module_eval do
         def identity_type
           self.annotation_types.select{|m| m.include? Entity::Identified }.last
@@ -50,6 +55,7 @@ module Entity
                         end
 
         return self if target_format == format
+
         if Array === self
           self.annotate(identifier_index(target_format, self.format).values_at(*self))
         else
@@ -73,8 +79,6 @@ module Entity
 
   end
 
-  attr_accessor :identifier_files, :formats, :default_format, :name_format, :description_format
-
   def add_identifiers(file, default = nil, name = nil, description = nil)
     if TSV === file
       all_fields = file.all_fields
@@ -88,6 +92,8 @@ module Entity
       end
     end
 
+    self.include Entity::Identified unless Entity::Identified === self
+
     self.format = all_fields
     @formats ||= []
     @formats.concat all_fields
@@ -100,9 +106,6 @@ module Entity
     @identifier_files ||= []
     @identifier_files << file
     @identifier_files.uniq!
-
-
-    self.include Entity::Identified unless Entity::Identified === self
   end
 
 end

data/lib/rbbt/knowledge_base/entity.rb

@@ -19,17 +19,26 @@ class KnowledgeBase
 
 
   def entity_options_for(type, database_name = nil)
-    options = entity_options[Entity.formats[type]] || {}
+    entity_options = self.entity_options
+    IndiferentHash.setup entity_options if entity_options and not IndiferentHash === entity_options
+    options = entity_options[type.to_s] || entity_options[Entity.formats[type.to_s].to_s] || {}
     options[:format] = @format[type] if @format.include? :type
     options = {:organism => namespace}.merge(options)
-    if database_name and 
-      (database = get_database(database_name)).entity_options and
-      (database = get_database(database_name)).entity_options[type]
-      options = options.merge database.entity_options[type] 
+    if database_name  
+      database = get_database(database_name)
+      if database.entity_options and (database.entity_options[type] or database.entity_options[Entity.formats[type.to_s].to_s])
+        options = options.merge(database.entity_options[type] || database.entity_options[Entity.formats[type.to_s].to_s])
+      end
     end
     options
   end
 
+  def annotate(entities, type, database = nil)
+    format = @format[type] || type
+    entity_options = entity_options_for(type, database)
+    Misc.prepare_entity(entities, format, entity_options)
+  end
+
   def translate(entities, type)
     if format = @format[type] and (entities.respond_to? :format and format != entities.format)
       entities.to format
@@ -38,11 +47,6 @@ class KnowledgeBase
     end
   end
 
-  def annotate(entities, type, database = nil)
-    format = @format[type] || type
-    Misc.prepare_entity(entities, format, entity_options_for(type, database))
-  end
-
   def source_type(name)
     Entity.formats[source(name)]
   end

data/lib/rbbt/knowledge_base/registry.rb

@@ -36,9 +36,11 @@ class KnowledgeBase
 
   def get_index(name, options = {})
     name = name.to_s
-    key = name.to_s + "_" + Misc.digest(Misc.fingerprint([name,options]))
-    @indices[key] ||= 
+    @indices[[name, options]] ||= 
       begin 
+        fp = Misc.fingerprint([name,options])
+        key = name.to_s + "_" + Misc.digest(fp)
+
         Persist.memory("Index:" << [key, dir] * "@") do
           options = options.dup
           persist_dir = dir
@@ -48,6 +50,14 @@ class KnowledgeBase
           options = Misc.add_defaults options, registered_options if registered_options and registered_options.any?
           options = Misc.add_defaults options, :persist_file => persist_file, :persist_dir => persist_dir, :namespace => namespace, :format => format, :persist => true
 
+          if entity_options
+            options[:entity_options] ||= {}
+            entity_options.each do |type, info|
+              options[:entity_options][type] ||= {}
+              options[:entity_options][type] = Misc.add_defaults options[:entity_options][type], info
+            end
+          end
+
           persist_options = Misc.pull_keys options, :persist
 
           index = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
@@ -81,6 +91,14 @@ class KnowledgeBase
           options = Misc.add_defaults options, registered_options if registered_options and registered_options.any?
           options = Misc.add_defaults options, :persist_file => persist_file, :namespace => namespace, :format => format, :persist => true
 
+          if entity_options
+            options[:entity_options] ||= {}
+            entity_options.each do |type, info|
+              options[:entity_options][type] ||= {}
+              options[:entity_options][type] = Misc.add_defaults options[:entity_options][type], info
+            end
+          end
+
           persist_options = Misc.pull_keys options, :persist
 
           database = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]

data/lib/rbbt/resource/path.rb

@@ -5,6 +5,7 @@ module Path
   attr_accessor :resource, :pkgdir, :search_paths
 
   def self.setup(string, pkgdir = nil, resource = nil, search_paths = nil)
+    string = string.dup if string.frozen?
     string.extend Path
     string.pkgdir = pkgdir || 'rbbt'
     string.resource = resource

data/lib/rbbt/resource/rake.rb

@@ -52,6 +52,7 @@ module Rake
         Log.exception $!
         Kernel.exit! -1
       end
+      Kernel.exit! 0
     }
     Process.waitpid(pid)
     raise "Rake failed" unless $?.success?

data/lib/rbbt/tsv/accessor.rb

@@ -84,7 +84,7 @@ module TSV
 
   def with_monitor(value = true)
     saved_monitor = @monitor
-    @monitor = value
+    @monitor = value.nil? ? false : value
     res = yield
     @monitor = saved_monitor
     res
@@ -471,10 +471,8 @@ module TSV
   end
 
   def namespace=(value)
-    #self.send(:[]=, "__tsv_hash_namespace", value.nil? ? SERIALIZED_NIL : TSV::TSV_SERIALIZER.dump(value), true)
     self.send(:[]=, "__tsv_hash_namespace", dump_entry_value(value), true)
     @namespace = value
-    @entity_options = nil
   end
 
   def fields=(value)

data/lib/rbbt/tsv/change_id.rb

@@ -89,7 +89,7 @@ module TSV
   def self.translation_index(files, target = nil, source = nil, options = {})
     return nil if source == target
     options = Misc.add_defaults options.dup, :persist => true
-    fields = source ? [source] : nil
+    fields = (source and not source.empty?) ? [source] : nil
     files.each do |file|
       if TSV === file
         all_fields = file.all_fields
@@ -117,7 +117,7 @@ module TSV
 
         common_field = (all_fields & other_all_fields).first
 
-        if common_field and (source.nil? or all_fields.include? source) and other_all_fields.include? target 
+        if common_field and (source.nil? or source.empty? or all_fields.include? source) and other_all_fields.include? target 
 
           index = Persist.persist_tsv(nil, Misc.fingerprint(files), {:files => files, :source => source, :target => target}, :prefix => "Translation index", :persist => options[:persist]) do |data|
 

data/lib/rbbt/tsv/manipulate.rb

@@ -253,15 +253,16 @@ module TSV
           case type 
           when :double
             new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
-              if current = data[key] 
+              if data[key] 
+                current = data[key].dup
                 value.each_with_index do |v, i|
-                  if _c = current[i]
-                    _c.concat v if v
+                  if current[i]
+                    current[i] += v if v
                   else
                     current[i] = v || []
                   end
                 end
-                data[key] = current if data.respond_to? :tokyocabinet_class
+                data[key] = current 
               else
                 data[key] = value.collect{|v| v.nil? ? nil : v.dup}
               end
@@ -269,7 +270,7 @@ module TSV
           when :flat
             new_key_field_name, new_field_names = through new_key_field, new_fields, uniq, zipped do |key, value|
               data[key] ||= []
-              data[key].concat value
+              data[key] += value
             end
           end
         end

data/lib/rbbt/tsv/parser.rb

@@ -523,6 +523,7 @@ module TSV
                else
                  stream.stat.size
                end
+        size = nil if size.to_i == 0
         desc = "Parsing Stream"
         step = 100
         if Hash === monitor

data/lib/rbbt/util/concurrency/processes/worker.rb

@@ -31,7 +31,6 @@ class RbbtProcessQueue
       rescue ClosedStream
       rescue Aborted, Interrupt
         Log.warn "Worker #{Process.pid} aborted"
-        Kernel.exit! 0
       rescue Exception
         Log.exception $!
         @callback_queue.push($!) if @callback_queue
@@ -39,6 +38,7 @@ class RbbtProcessQueue
       ensure
         @callback_queue.close_write if @callback_queue 
       end
+      Kernel.exit! 0
     end
 
     def run_with_respawn(multiplier = nil)

data/lib/rbbt/util/misc/pipes.rb

@@ -64,6 +64,7 @@ module Misc
           Process.kill :INT, parent_pid
           Kernel.exit! -1
         end
+        Kernel.exit! 0
       }
       sin.close 
       ConcurrentStream.setup sout, :pids => [pid]

data/lib/rbbt/workflow/step/run.rb

@@ -409,7 +409,9 @@ class Step
     if stream
       begin
         Misc.consume_stream stream 
+        stream.join if stream.respond_to? :join
       rescue Exception
+        stream.abort
         self._abort
         raise $!
       end
@@ -427,7 +429,7 @@ class Step
 
     grace
 
-    join_stream if status == :streaming
+    join_stream if status.to_s == "streaming"
 
     return self if not Open.exists? info_file
 

data/share/rbbt_commands/tsv/info

@@ -42,7 +42,7 @@ when options[:tokyocabinet_bd]
   tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
   puts tsv.summary
 else
-  header = TSV.parse_header(Open.open(file), options)
+  header = TSV.parse_header(Open.open(file, :nocache => true), options)
 
   puts "File: #{ file }"
   puts "Type: #{header.type}"

data/test/rbbt/association/test_index.rb

@@ -78,5 +78,12 @@ TP53 NFKB1|GLI1 activation|activation true|true
     assert tsv.match("TP53").length > 10
   end
 
+  def test_index_flat_to_matrix
+    require 'rbbt/sources/tfacts'
+    file = TFacts.regulators
+    tsv = Association.index(file,  :type => :flat, :source => "Transcription Factor Associated Gene Name=~Associated Gene Name", :merge => true)
+    assert(tsv.to_matrix(false))
+  end
+
 
 end

data/test/rbbt/association/test_open.rb

@@ -55,7 +55,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
   end
 
   def test_index_persist_reverse
-    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge(:source => "TG", :target => "SG=~Associated Gene Name"), :persist => true).reverse
+    tsv = Association.index(EFFECT, EFFECT_OPTIONS.merge( :source => "TG", :target => "SG=~Associated Gene Name"), :persist => true).reverse
     tsv.unnamed = false
     assert_equal "inhibition", tsv["MDM2~TP53"]["Effect"]
     assert_equal %w(MDM2~TP53), tsv.match("MDM2")

data/test/rbbt/knowledge_base/test_entity.rb

@@ -0,0 +1,41 @@
+require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+require 'rbbt/knowledge_base'
+require 'rbbt/knowledge_base/entity'
+
+module Gene
+  extend Entity
+end
+
+class TestKnowledgeEnity < Test::Unit::TestCase
+
+  EFFECT =StringIO.new <<-END
+#: :sep=" "#:type=:double
+#SG TG Effect
+MDM2 TP53 inhibition
+TP53 NFKB1|GLI1 activation|activation true|true
+  END
+
+  EFFECT_OPTIONS = {
+    :source => "SG=~Associated Gene Name",
+    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
+    :undirected => true,
+    :persist => true,
+    :namespace => "Hsa"
+  }
+  Gene.add_identifiers datafile_test('identifiers')
+
+  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
+
+  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
+  KNOWLEDGE_BASE.format = {"Gene" => "Associated Gene Name"}
+
+  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
+
+  def test_entity_options
+    KNOWLEDGE_BASE.entity_options = {"Gene" => {:organism => "Mmu"}}
+    assert_equal "Mmu", KNOWLEDGE_BASE.children(:effects, "TP53").target_entity.organism
+  end
+end
+

data/test/rbbt/knowledge_base/test_registry.rb

@@ -73,9 +73,10 @@ TP53 NFKB1|GLI1 activation|activation true|true
     assert_equal count, count2
   end
 
-
   def test_pina2
+    KNOWLEDGE_BASE.entity_options["Gene"] = {:organism => "Mmu"}
     index = KNOWLEDGE_BASE.get_index(:pina, :persist => true, :source_format => "Ensembl Gene ID", :target_format => "Ensembl Gene ID", :undirected => true)
+    assert_equal "Mmu", index.entity_options["Gene"][:organism]
   end
 end
 

data/test/rbbt/knowledge_base/test_syndicate.rb

@@ -0,0 +1,48 @@
+require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+require 'rbbt/knowledge_base'
+require 'rbbt/knowledge_base/query'
+
+module Gene
+  extend Entity
+end
+class TestKnowledgeBaseSyndicate < Test::Unit::TestCase
+
+  EFFECT =StringIO.new <<-END
+#: :sep=" "#:type=:double
+#SG TG Effect
+MDM2 TP53 inhibition
+TP53 NFKB1|GLI1 activation|activation true|true
+  END
+
+  EFFECT_OPTIONS = {
+    :source => "SG=~Associated Gene Name",
+    :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
+    :persist => false,
+    :identifiers => datafile_test('identifiers'),
+    :undirected => true,
+    :namespace => "Hsa"
+  }
+
+  EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
+
+  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
+  KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
+  KNOWLEDGE_BASE.entity_options["Gene"] = {:organism => "Mmu", :test_option => "TEST"}
+
+  KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
+
+  def test_syndicate_entity_options
+    Gene.add_identifiers datafile_test('identifiers')
+    kb = KnowledgeBase.new "/tmp/kb.foo3", "Hsa"
+    kb.format = {"Gene" => "Associated Gene Name"} 
+    kb.syndicate :orig, KNOWLEDGE_BASE
+    assert_equal "Mmu", KNOWLEDGE_BASE.entity_options_for("Gene", "effects")[:organism]
+    assert_equal "Mmu", kb.get_index("effects@orig").entity_options["Gene"][:organism]
+    assert_equal "Mmu", kb.get_database("effects@orig").entity_options["Gene"][:organism]
+    assert_equal "Mmu", kb.entity_options_for("Gene", "effects@orig")[:organism]
+    assert_equal "Mmu", kb.children("effects@orig", "TP53").source_entity.organism
+  end
+end
+

data/test/rbbt/test_entity.rb

@@ -12,6 +12,7 @@ class TestA
   end
 end
 
+Entity.entity_property_cache = Rbbt.tmp.test.entity_property.find
 module ReversableString
   extend Entity
 
@@ -21,7 +22,7 @@ module ReversableString
     $count += 1
     self.collect{|s| s.reverse}
   end
- 
+
   property :reverse_text_single => :single do
     $count += 1
     self.reverse
@@ -31,7 +32,7 @@ module ReversableString
     $count += 1
     self.collect{|s| s.reverse}
   end
- 
+
   property :reverse_text_single_p => :single do
     $count += 1
     self.reverse
@@ -51,11 +52,10 @@ module ReversableString
       ReversableString.setup(c)
     }
   end
- 
-  persist :reverse_text_ary_p
-  persist :reverse_text_ary_p
-  persist :reverse_text_ary_p
-  persist :reverse_text_single_p
+
+  persist :reverse_text_ary_p, :string
+  persist :reverse_text_single_p, :memory
+  #persist :_single_reverse_text_single_p, :string
 
   persist :reverse_text_ary_p_array, :array, :dir => TmpFile.tmp_file
 
@@ -64,7 +64,7 @@ end
 
 class TestEntity < Test::Unit::TestCase
 
-  def test_property_ary
+  def _test_property_ary
     a = ["String1", "String2"]
     ReversableString.setup(a)
 
@@ -84,7 +84,7 @@ class TestEntity < Test::Unit::TestCase
     end
   end
 
-  def test_property_single
+  def _test_property_single
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -96,7 +96,7 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 3, $count
   end
 
-  def test_property_ary_p
+  def _test_property_ary_p
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -114,15 +114,23 @@ class TestEntity < Test::Unit::TestCase
     $count = 0
 
     assert_equal "2gnirtS", a.reverse_text_single_p.last
+
     assert_equal 2, $count
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_single_p.last
+    assert_equal 0, $count
     assert_equal "2gnirtS", a[1].reverse_text_single_p
-    assert_equal 2, $count
+    assert_equal 0, $count
   end
 
-  def test_property_ary_p_array
+  def _test_property_ary_p_array
     a = ["String1", "String2"]
     ReversableString.setup a
 
+    assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
+
     $count = 0
 
     assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
@@ -131,7 +139,7 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 1, $count
   end
 
-  def test_unpersist
+  def _test_unpersist
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -160,14 +168,14 @@ 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
     assert_equal string.length, string.annotation_list.length
   end
 
-  def test_clean_annotations
+  def _test_clean_annotations
 
     string = "test_string"
     ReversableString.setup string

data/test/test_helper.rb

@@ -14,9 +14,10 @@ class Test::Unit::TestCase
 
   def setup
     Random.new
-    if defined? Persist
-      Persist.cachedir = Rbbt.tmp.test.persistence.find :user
-    end
+
+    Persist.cachedir = Rbbt.tmp.test.persistence.find :user if defined? Persist
+
+    Entity.entity_property_cache = Rbbt.tmp.test.entity_property.find(:user) if defined? Entity
   end
 
   def teardown
@@ -25,11 +26,16 @@ class Test::Unit::TestCase
     #  Persist::CONNECTIONS.values.each do |c| c.close end
     #  Persist::CONNECTIONS.clear
     #end
+
+    #if defined? Entity
+    #  FileUtils.rm_rf Entity.entity_property_cache.find(:user) if Entity.entity_property_cache =~ /tmp\/test/
+    #end
   end
 
   def self.datafile_test(file)
     Path.setup(File.join(File.dirname(__FILE__), 'data', file.to_s))
   end
+
   def datafile_test(file)
     Test::Unit::TestCase.datafile_test(file)
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.35
+  version: 5.14.36
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-14 00:00:00.000000000 Z
+date: 2014-10-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -326,6 +326,7 @@ files:
 - test/rbbt/knowledge_base/test_entity.rb
 - test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
 - test/rbbt/persist/test_tsv.rb
 - test/rbbt/persist/tsv/test_cdb.rb
 - test/rbbt/persist/tsv/test_kyotocabinet.rb
@@ -448,6 +449,7 @@ test_files:
 - test/rbbt/knowledge_base/test_registry.rb
 - test/rbbt/knowledge_base/test_entity.rb
 - test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
 - test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb