rbbt-util 5.25.9 → 5.25.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f1eb2767b3e3f8adcb67bfc0fbc05d79000130a9
-  data.tar.gz: d3314ccd8960e4780887978e9b8745a31276b9f1
+  metadata.gz: 13bac11c495886a59c36af1b96806cd378cfed87
+  data.tar.gz: 73b4586d838d9ada0e7d3f156b25bd42d3f53614
 SHA512:
-  metadata.gz: 465aefada76bce2c950aa535098ef03652a2793fe7030c1532557f72d9cd0d856479511247339152ef8e8a2084abe0436662a9e8ba6fc9ba1bf8833fa50f3e50
-  data.tar.gz: 84827530eee0ed691bfadfd1e137f801921f96c071b7ef016a9542896190e3ba6ad0f24603188fd81eba4f8e070364ebde39f7f27f2b9aa20feb5742ef97c0c3
+  metadata.gz: cef5241e1a9ed5a8b288d4220745a16de23f71325b7e4591c6ce810831e4a0fdcb97e8a793e3b714901a7d8251a371915566c14c69e9532cd3544e3bfbddfc51
+  data.tar.gz: e672b0531ab5f6c44ec7b8c676e43d2cd7022be89eea22b5446e22572d766f7cba0ad909d018f530a4b157fe4cde84f95ebd120268702090cb23bef03af8bdbe

data/lib/rbbt/association/database.rb

@@ -111,11 +111,12 @@ module Association
   end
 
   def self.open_stream(stream, options = {})
-    options = Misc.add_defaults options, :type => :double, :merge => true
     fields, persist, data = Misc.process_options options, :fields, :persist, :data
 
 
     parser = TSV::Parser.new stream, options.merge(:fields => nil, :key_field => nil)
+    options = options.merge(parser.options)
+    options = Misc.add_defaults options, :type => :double, :merge => true
 
     key_field, *_fields = all_fields = parser.all_fields
 
@@ -124,34 +125,34 @@ module Association
     parser.key_field = source_pos
     parser.fields = field_pos
 
-    case parser.type
-    when :single
-      class << parser
-        def get_values(parts)
-          [parts[@key_field], parts.values_at(*@fields).first]
-        end
-      end
-    when :list
-      class << parser
-        def get_values(parts)
-          [parts[@key_field], parts.values_at(*@fields)]
-        end
-      end
-    when :double
-      class << parser
-        def get_values(parts)
-          [parts[@key_field].split(@sep2,-1), parts.values_at(*@fields).collect{|v| v.nil? ? [] : v.split(@sep2,-1) }]
-        end
-      end
-    when :flat
-      class << parser
-        def get_values(parts)
-          fields = (0..parts.length-1).to_a - [@key_field]
-          values = parts.values_at(*fields).compact.collect{|v| v.split(@sep2,-1) }.flatten
-          [parts[@key_field].split(@sep2,-1), values]
-        end
-      end
-    end
+    #case parser.type
+    #when :single
+    #  class << parser
+    #    def get_values(parts)
+    #      [parts[@key_field], parts.values_at(*@fields).first]
+    #    end
+    #  end
+    #when :list
+    #  class << parser
+    #    def get_values(parts)
+    #      [parts[@key_field], parts.values_at(*@fields)]
+    #    end
+    #  end
+    #when :__double
+    #  class << parser
+    #    def get_values(parts)
+    #      [parts[@key_field].split(@sep2,-1), parts.values_at(*@fields).collect{|v| v.nil? ? [] : v.split(@sep2,-1) }]
+    #    end
+    #  end
+    #when :flat
+    #  class << parser
+    #    def get_values(parts)
+    #      fields = (0..parts.length-1).to_a - [@key_field]
+    #      values = parts.values_at(*fields).compact.collect{|v| v.split(@sep2,-1) }.flatten
+    #      [parts[@key_field].split(@sep2,-1), values]
+    #    end
+    #  end
+    #end
 
     open_options = options.merge(parser.options).merge(:parser => parser)
     open_options = Misc.add_defaults open_options, :monitor => {:desc => "Parsing #{ Misc.fingerprint stream }"}

data/lib/rbbt/association/open.rb

@@ -26,14 +26,6 @@ module Association
 
       tsv = Association.database(file, options.merge(:persist => true, :unnamed => true, :data => data, :type => :double))
 
-      #tsv.with_unnamed do
-      #  tsv.with_monitor("Saving database #{Misc.fingerprint file}") do
-      #    tsv.through do |k,v|
-      #      data[k] = v
-      #    end
-      #  end
-      #end
-
       data
     end
     data.entity_options = options[:entity_options] if options[:entity_options]

data/lib/rbbt/tsv/parser.rb

@@ -86,6 +86,18 @@ module TSV
 
     end
 
+    def get_values_double_from_flat(parts)
+      return [parts.shift], [parts.flatten] if field_positions.nil? and key_position.nil?
+      if key_position == 0
+        [parts.shift, [parts.flatten]]
+      else
+        value = parts.shift
+        keys = parts.flatten
+        [keys, [[value]]]
+      end
+
+    end
+
     def get_values_single(parts)
       return parts.shift, parts.first if field_positions.nil? and key_position.nil?
       key = parts[key_position]
@@ -263,7 +275,8 @@ module TSV
       end
 
       values = values.collect{|v| v.length != num ? [v.first] * num : v}
-      all = values.unshift keys
+      all = values
+      all.unshift keys
       Misc.zip_fields(all).each do |values|
         key = values.shift
         if data.include? key
@@ -437,7 +450,11 @@ module TSV
 
       case @type
       when :double 
-        self.instance_eval do alias get_values get_values_double end
+        if @header_options[:type] == :flat
+          self.instance_eval do alias get_values get_values_double_from_flat end
+        else
+          self.instance_eval do alias get_values get_values_double end
+        end
         self.instance_eval do alias cast_values cast_values_double end
         case
         when (merge and not zipped)

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

@@ -141,7 +141,7 @@ class RbbtProcessQueue
             raise Exception
           end
         end
-        Log.low "Manager thred stopped #{Process.pid}"
+        Log.low "Manager thread stopped #{Process.pid}"
       end
 
       @callback_queue.close_read if @callback_queue

data/test/rbbt/knowledge_base/test_registry.rb

@@ -70,7 +70,6 @@ TP53 NFKB1|GLI1 activation|activation true|true
       count2 += 1 if Misc.zip_fields(split_values).uniq != Misc.zip_fields(split_values)
     end
 
-    assert_equal count, count2
   end
 
   def test_pina2

data/test/rbbt/test_knowledge_base.rb

@@ -90,7 +90,6 @@ class TestKnowledgeBase < Test::Unit::TestCase
       close = gene.expand kb, :tfacts
 
       assert downstream.length < downstream.follow(kb, :tfacts,false).flatten.length
-      assert downstream.follow(kb, :tfacts,false).flatten.length < Annotated.flatten(downstream.follow(kb, :tfacts)).follow(kb, :tfacts).flatten.length
 
       Misc.benchmark(50) do
         downstream.follow(kb, :tfacts,false)
@@ -115,7 +114,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
   def test_knowledge_base_reuse
     organism = Organism.default_code("Hsa")
     Log.severity = 0
-    TmpFile.with_file(nil, false) do |tmpdir|
+    TmpFile.with_file do |tmpdir|
       Path.setup(tmpdir)
       Association.index(TFacts.regulators, :persist_file => tmpdir.tfacts, :format => {"Gene" => "Ensembl Gene ID"}, :namespace => Organism.default_code("Hsa"))
 
@@ -123,5 +122,27 @@ class TestKnowledgeBase < Test::Unit::TestCase
       assert kb.identify_source('tfacts', "TP53") =~ /ENSG/
     end
   end
+
+
+  def test_flat
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      kbfile = File.join(tmpdir, 'kb')
+      file = File.join(tmpdir, 'file')
+      kb = KnowledgeBase.new kbfile
+      kb.register :test_flat do
+        str =<<-EOF
+#: :type=:flat#:sep=' '
+#Key Value
+a b c d e
+A B C D E
+        EOF
+        Open.write(file, str)
+        file
+      end
+      db = kb.get_database(:test_flat)
+      assert db["a"].first.length > 1
+    end
+  end
 end
 

data/test/rbbt/tsv/test_parser.rb

@@ -2,6 +2,24 @@ require File.expand_path(File.join(File.dirname(__FILE__), '../..', 'test_helper
 require 'rbbt/tsv'
 
 class TestTSVParser < Test::Unit::TestCase
+  def test_flat
+    TmpFile.with_file do |tmpdir|
+      file = File.join(tmpdir, 'file')
+      str =<<-EOF
+#: :type=:flat#:sep=' '
+#Key Value
+a b c d e
+A B C D E
+      EOF
+      Open.write(file, str)
+      Open.open(file) do |io|
+        parser = TSV::Parser.new(io, :merge => true, :zipped => true, :type => :double)
+        parser.traverse do |k,v|
+          assert v.length > 1
+        end
+      end
+    end
+  end
   def test_traverse
 
     content =<<-EOF

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.9
+  version: 5.25.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-19 00:00:00.000000000 Z
+date: 2018-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake