rbbt-util 5.14.8 → 5.14.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d676e9769e4e13d664c42a65e74ec8c7d70bbe63
-  data.tar.gz: f3a75c5456360ae6e31d713ef964650adcb2edb4
+  metadata.gz: a2e935c66915d12e54d8a483af1f3ab9c0447c9c
+  data.tar.gz: 014e991d3c4c8769e4ff480e0a9566a65f84a160
 SHA512:
-  metadata.gz: e2cb4d0761e9b44f8d108888a966b874f572f144b16620754c6551349fc8c8d04ee061393e7032d829a3fa1f0e72a04185e5f6af3d5c264d4582daf7524063e9
-  data.tar.gz: 8402954673614b9b0ff6c4b73237a47d1f077ef795f9c452f96fab732e665428cb470e2ae38c12ed3c818c0c1b2d512d8322444020ba3b1783e528c30ce8a048
+  metadata.gz: 19e5dfaf77d8755695c2bed2c0f379eb3421e7b021e93e2caaa551ccc304ad70f1c91c892d096f6d3abe689f84a6a6d43260c2d68c4b0b4c1a9ac8cb946bca81
+  data.tar.gz: 402865585352cc0dfd319d84c40d125ee04eabab5105ea7039c05ea018ed709b27e1efb6d059da3260c8e1f78c47d1e439206cb59cfc79b5de09ce8b36eb2227

data/lib/rbbt/association.rb

@@ -14,22 +14,15 @@ module Association
 
     new = tsv.dup
     tsv.with_unnamed do
-      tsv.through do |key, values|
-        Misc.zip_fields(values).each do |zipped|
-          target, *rest = zipped
-
-          target_values = new[target] || []
-          if target_values and target_values.any?
-            zipped_target_values = Misc.zip_fields(target_values) 
-
-            zipped_target_values << ([key].concat rest)
-
-            new_values = Misc.zip_fields zipped_target_values
+      tsv.through do |source, values|
+        Misc.zip_fields(values).each do |_target_values|
+          target, *target_values = _target_values
+          if new[target].nil?
+            new[target] = [[source]] + target_values.collect{|v| [v] }
           else
-            new_values = [[key], rest.collect{|v| [v]}]
+            new[target].first << source
+            new[target][1..-1].zip(target_values).each{|list,elem| list << elem }
           end
-
-          new[target] = new_values
         end
       end
     end

data/lib/rbbt/association/index.rb

@@ -38,6 +38,8 @@ module Association
 
                      Association::Index.setup new
 
+                     new.undirected = undirected
+
                      new
                    end
     end
@@ -80,13 +82,12 @@ module Association
         matches = source.uniq.inject([]){|acc,e| acc.concat(match(e)) }
       end
 
-      return matches if target.nil? or target == :all or target == "all"
+      return matches if target == :all or target == "all"
 
       target_matches = {}
 
       matches.each{|code| 
         s,sep,t = code.partition "~"
-        next if (undirected and t > s) 
         target_matches[t] ||= []
         target_matches[t] << code
       }
@@ -96,11 +97,9 @@ module Association
 
     def subset_entities(entities)
       source, target = select_entities(entities)
-      source = :all if source.nil? and target.nil?
-      raise "Please specify source entities" if source.nil?
-      target = :all if target.nil?
-      return if Array === target and target.empty?
-      return if Array === source and source.empty?
+      return [] if source.nil? or target.nil?
+      return [] if Array === target and target.empty?
+      return [] if Array === source and source.empty?
       subset source, target
     end
   end

data/lib/rbbt/association/item.rb

@@ -7,6 +7,10 @@ module AssociationItem
   annotation :database
   annotation :reverse
 
+  property :namespace => :both do
+    knowledge_base.namespace
+  end
+
   property :part => :array2single do
     self.clean_annotations.collect{|p| p.partition("~") }
   end
@@ -19,11 +23,11 @@ module AssociationItem
     self.clean_annotations.collect{|p| p[/[^~]+/] }
   end
 
-  property :target_type => :single do
-    reverse ? knowledge_base.source(database) : knowledge_base.target(database)
+  property :target_type => :both do
+    type = reverse ? knowledge_base.source(database) : knowledge_base.target(database)
   end
 
-  property :source_type => :single do
+  property :source_type => :both do
     reverse ? knowledge_base.target(database) : knowledge_base.source(database)
   end
 
@@ -42,8 +46,13 @@ module AssociationItem
     value.collect{|v| NamedArray.setup(v, knowledge_base.get_index(database).fields)}
   end
 
+  property :info_fields => :both do
+    knowledge_base.index_fields(database)
+  end
+
   property :info => :array2single do
-    fields = knowledge_base.index_fields(database)
+    fields = self.info_fields
+
     return [{}] * self.length if fields.nil? or fields.empty?
 
     value = self.value

data/lib/rbbt/knowledge_base.rb

@@ -15,6 +15,11 @@ class KnowledgeBase
     end
   end
 
+
+  def setup(name, matches, reverse = false)
+    AssociationItem.setup matches, self, name, reverse
+  end
+
   attr_accessor :namespace, :dir, :indices, :registry, :format, :databases, :entity_options
   def initialize(dir, namespace = nil)
     @dir = Path.setup(dir).find
@@ -260,10 +265,6 @@ class KnowledgeBase
 
   #{{{ Query
   
-  def setup(name, matches, reverse = false)
-    AssociationItem.setup matches, self, name, reverse
-  end
-
   def all(name, options={})
     repo = get_index name, options
     setup name, repo.keys

data/share/rbbt_commands/workflow/server

@@ -10,6 +10,7 @@ require 'rbbt/rest/main'
 require 'rbbt/rest/entity'
 require 'rbbt/rest/workflow'
 require 'rbbt/rest/file_server'
+require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 
 options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*"
@@ -34,6 +35,7 @@ class WorkflowRest < Sinatra::Base
   register Sinatra::RbbtRESTMain
   register Sinatra::RbbtRESTWorkflow
   register Sinatra::RbbtRESTEntity
+  register Sinatra::RbbtRESTKnowledgeBase
   helpers Sinatra::RbbtMiscHelpers
 
   #{{{ DIRECTORIES

data/test/rbbt/test_association.rb

@@ -57,6 +57,9 @@ class TestAssociations < Test::Unit::TestCase
     assert_equal ["aa"], database["TP53"].first
   end
 
+  def test_reciprocal
+  end
+
 
   def __test_ICGC
     assoc = Association.open(Open.open('ftp://data.dcc.icgc.org/current/Chronic_Lymphocytic_Leukemia-ISC_MICINN-ES/simple_somatic_mutation.CLLE-ES.tsv.gz'),

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.8
+  version: 5.14.9
 platform: ruby
 authors:
 - Miguel Vazquez