rbbt-util 5.5.6 → 5.5.7

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/rbbt/association.rb

@@ -68,7 +68,7 @@ module Association
   
   def self.open_tsv(file, source, source_header, target, target_header, all_fields, options)
     fields = all_fields.dup
-    fields.delete source
+    fields.delete source 
     fields.delete target
     fields.unshift target
 
@@ -87,9 +87,11 @@ module Association
 
     tsv = case file
           when TSV
-            file.fields == field_headers ? 
-              file :
+            if file.fields == field_headers
+              file
+            else
               file.reorder(source, field_headers)
+            end
           else
             TSV.open(file, open_options)
           end
@@ -169,7 +171,7 @@ module Association
 
     target, target_header, orig_target_format = calculate_headers(key_field, fields, target_spec)
     target_format ||= orig_target_format 
-    target = (([key_field] + fields) - [source]).first if target.nil?
+    target = (key_field == source ? fields.first : (([key_field] + fields) - [source]).first) if target.nil?
     target = key_field if target == :key
     target_header ||= target
 
@@ -201,9 +203,9 @@ module Association
 
     source, source_header, source_format, target, target_header, target_format = specs(all_fields, options)
  
-    Log.info("Loading associations from: #{ Misc.fingerprint file }")
-    Log.info("sources: #{ [source, source_header, source_format].join(", ") }")
-    Log.info("targets: #{ [target, target_header, target_format].join(", ") }")
+    Log.low("Loading associations from: #{ Misc.fingerprint file }")
+    Log.low("sources: #{ [source, source_header, source_format].join(", ") }")
+    Log.low("targets: #{ [target, target_header, target_format].join(", ") }")
 
     tsv = open_tsv(file, source, source_header, target, target_header, all_fields, options)
 
@@ -229,8 +231,13 @@ module Association
 
       tsv.annotate(data)
       data.serializer = tsv.type if TokyoCabinet::HDB === data
-      data.merge! tsv
-      tsv.annotate data
+
+      tsv.with_unnamed do
+        tsv.each do |k,v|
+          next if v.nil?
+          data[k] = v
+        end
+      end
 
       data
     end
@@ -238,9 +245,9 @@ module Association
 
   #{{{ Index
 
-  def self.get_index(index_file, write = false)
-    Persist.open_tokyocabinet(index_file, write, :list, TokyoCabinet::BDB).tap{|r| r.unnamed = true; Association::Index.setup r }
-  end
+  #def self.get_index(index_file, write = false)
+  #  Persist.open_tokyocabinet(index_file, write, :list, TokyoCabinet::BDB).tap{|r| r.unnamed = true; Association::Index.setup r }
+  #end
 
   def self.index(file, options = {}, persist_options = {})
     options = {} if options.nil?

data/lib/rbbt/knowledge_base.rb

@@ -45,6 +45,7 @@ class KnowledgeBase
  
   def register(name, file = nil, options = {}, &block)
     if block_given?
+      block.define_singleton_method(:filename) do name.to_s end
       Log.debug("Registering #{ name } from code block")
       @registry[name] = [block, options]
     else
@@ -53,10 +54,20 @@ class KnowledgeBase
     end
   end
 
+  def syndicate(kb, name)
+    kb.all_databases.each do |database|
+      db_name = [database, name] * "@"
+      register(db_name) do
+        kb.get_database(database)
+      end
+    end
+  end
+
   def all_databases
     (@indices.keys + @registry.keys).uniq
   end
 
+
   def description(name)
     @descriptions[name] ||= get_index(name).key_field.split("~")
   end
@@ -100,6 +111,7 @@ class KnowledgeBase
   end
  
   def get_database(name, options = {})
+    options = Misc.add_defaults options, :persist_dir => dir.databases
     persist_options = Misc.pull_keys options, :persist
 
     file, registered_options = registry[name]
@@ -107,7 +119,7 @@ class KnowledgeBase
     raise "Repo #{ name } not found and not registered" if file.nil?
 
     @databases[name] ||= begin 
-                           Log.debug "Opening database #{ name } from #{ Misc.fingerprint file }. #{options}"
+                           Log.low "Opening database #{ name } from #{ Misc.fingerprint file }. #{options}"
                            Association.open(file, options, persist_options).
                              tap{|tsv| tsv.namespace = self.namespace}
                          end
@@ -115,6 +127,7 @@ class KnowledgeBase
 
  
   def get_index(name, options = {})
+    options = Misc.add_defaults options, :persist_dir => dir.indices
     persist_options = Misc.pull_keys options, :persist
 
     file, registered_options = registry[name]
@@ -122,7 +135,7 @@ class KnowledgeBase
     raise "Repo #{ name } not found and not registered" if file.nil?
 
     @indices[name] ||= begin 
-                           Log.debug "Opening index #{ name } from #{ Misc.fingerprint file }. #{options}"
+                           Log.low "Opening index #{ name } from #{ Misc.fingerprint file }. #{options}"
                            Association.index(file, options, persist_options).
                              tap{|tsv| tsv.namespace = self.namespace}
                          end

data/lib/rbbt/util/log.rb

@@ -19,7 +19,7 @@ module Log
 
   WHITE, DARK, GREEN, YELLOW, RED = ["0;37m", "0m", "0;32m", "0;33m", "0;31m"].collect{|e| "\033[#{e}"}
 
-  SEVERITY_COLOR = [WHITE, GREEN, YELLOW, RED,WHITE, GREEN, YELLOW].collect{|e| "\033[#{e}"}
+  SEVERITY_COLOR = [WHITE, GREEN, YELLOW, RED, GREEN, YELLOW, ERROR].collect{|e| "\033[#{e}"}
 
   def self.log(message = nil, severity = MEDIUM, &block)
     message ||= block

data/test/rbbt/test_knowledge_base.rb

@@ -91,7 +91,6 @@ class TestKnowledgeBase < Test::Unit::TestCase
     found = Genomics.knowledge_base.identify :pina, gene
     p53_interactors = Misc.profile{ Genomics.knowledge_base.children(:pina, found).target_entity }
 
-    ddd p53_interactors.length
 
     Misc.profile do
       puts Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).length
@@ -100,5 +99,13 @@ class TestKnowledgeBase < Test::Unit::TestCase
     #assert Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).target_entities.name.include? "MDM2"
   end
 
+  def test_syndication
+    kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
+    kb.syndicate @kb, :genomics
+
+    gene = "TP53"
+    found = kb.identify "pina@genomics", gene
+    assert found =~ /ENSG/
+  end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.6
+  version: 5.5.7
 platform: ruby
 authors:
 - Miguel Vazquez