rbbt-util 5.13.1 → 5.13.2

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -4,7 +4,7 @@ require 'rbbt/tsv/parallel'
 
 class TestTSVParallelThrough < Test::Unit::TestCase
 
-  def test_traverse_tsv
+  def _test_traverse_tsv
     require 'rbbt/sources/organism'
 
     head = 100
@@ -23,7 +23,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
-  def test_traverse_tsv_cpus
+  def _test_traverse_tsv_cpus
     require 'rbbt/sources/organism'
 
     head = 100
@@ -45,7 +45,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert res.values.compact.flatten.uniq.length > 0
   end
 
-  def test_traverse_stream
+  def _test_traverse_stream
     require 'rbbt/sources/organism'
 
     head = 1000
@@ -59,7 +59,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
-  def test_traverse_stream_cpus
+  def _test_traverse_stream_cpus
     require 'rbbt/sources/organism'
 
     head = 1000
@@ -73,7 +73,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
-  def test_traverse_stream_keys
+  def _test_traverse_stream_keys
     require 'rbbt/sources/organism'
 
     head = 1000
@@ -97,7 +97,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal res.sort, Organism.identifiers("Hsa").tsv(:head => head).keys.sort
   end
   
-  def test_traverse_array
+  def _test_traverse_array
     require 'rbbt/sources/organism'
 
     array = []
@@ -119,7 +119,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal array, res
   end
 
-  def test_traverse_array_threads
+  def _test_traverse_array_threads
     require 'rbbt/sources/organism'
 
     array = []
@@ -140,7 +140,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal array.sort, res.sort
   end
 
-  def test_traverse_array_cpus
+  def _test_traverse_array_cpus
     require 'rbbt/sources/organism'
 
     array = []
@@ -155,7 +155,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal array.sort, res.sort
   end
 
-  def test_traverse_benchmark
+  def _test_traverse_benchmark
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -177,7 +177,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     end
   end
 
-  def test_traverse_into_dumper
+  def _test_traverse_into_dumper
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -195,7 +195,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.size
   end
 
-  def test_traverse_into_dumper_threads
+  def _test_traverse_into_dumper_threads
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -215,7 +215,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.size
   end
 
-  def test_traverse_into_dumper_cpus
+  def _test_traverse_into_dumper_cpus
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -236,7 +236,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
 
   #{{{ TRAVERSE DUMPER
 
-  def test_traverse_dumper
+  def _test_traverse_dumper
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -257,7 +257,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.size
   end
 
-  def test_traverse_dumper_threads
+  def _test_traverse_dumper_threads
     require 'rbbt/sources/organism'
 
     head = 2_000
@@ -279,7 +279,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.size
   end
 
-  def test_traverse_dumper_cpus
+  def _test_traverse_dumper_cpus
     require 'rbbt/sources/organism'
 
     head = 10_000
@@ -307,29 +307,26 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
     cpus = 2
 
-    stream = Organism.identifiers("Hsa/jun2011").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa/jun2011").tsv_options
 
-    assert_raise do
-      begin
-      TSV.traverse stream, :head => head,  :cpus => cpus, :into => dumper do |k,v|
-        k = k.first
-        raise "STOP" if rand(100) < 1
-        [k,v]
-      end
-      stream = dumper.stream
-      stream.read
-      stream.join
-      rescue Exception
-        Log.exception $!
-        stream.abort if stream.respond_to? :abort
-        stream.join if stream.respond_to? :join
-        raise $!
+    3.times do
+      stream = Organism.identifiers("Hsa/jun2011").open 
+      dumper = TSV::Dumper.new Organism.identifiers("Hsa/jun2011").tsv_options
+      dumper.init
+
+      assert_raise do
+        TSV.traverse stream, :head => head,  :cpus => cpus, :into => dumper do |k,v|
+          k = k.first
+          raise "STOP" if rand(100) < 1
+          [k,v]
+        end
+        stream = dumper.stream
+        stream.read
+        stream.join
       end
     end
   end
 
-  def test_traverse_into_stream
+  def _test_traverse_into_stream
     size = 100
     array = (1..size).to_a.collect{|n| n.to_s}
     stream = TSV.traverse array, :into => :stream do |e|
@@ -338,7 +335,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal size, stream.read.split("\n").length
   end
 
-  def test_traverse_progress
+  def _test_traverse_progress
     size = 1000
     array = (1..size).to_a.collect{|n| n.to_s}
     stream = TSV.traverse array, :bar => {:max => size, :desc => "Array"}, :cpus => 5, :into => :stream do |e|

data/test/rbbt/tsv/test_filter.rb

@@ -3,7 +3,7 @@ require 'rbbt/tsv'
 require 'rbbt/tsv/filter'
 
 class TestTSVFilters < Test::Unit::TestCase
-  def test_collect
+  def _test_collect
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB
@@ -19,7 +19,7 @@ row2    A    B
     end
   end
 
-  def test_through
+  def _test_through
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB
@@ -37,7 +37,7 @@ row2    A    B
     end
   end
 
-  def test_2_filters
+  def _test_2_filters
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB
@@ -64,7 +64,7 @@ row3    A    C
     end
   end
 
-  def test_filter_persistence
+  def _test_filter_persistence
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB
@@ -98,7 +98,7 @@ row3    A    C
     end
   end
 
-  def test_filter_persistence_update
+  def __test_filter_persistence_update
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB
@@ -165,7 +165,7 @@ row2 A B C
     end
   end
 
-  def test_filename
+  def _test_filename
     content1 =<<-EOF
 #: :sep=/\\s+/#:case_insensitive=false
 #Id    ValueA    ValueB

data/test/rbbt/util/concurrency/test_processes.rb

@@ -70,7 +70,6 @@ class TestConcurrencyProcess < Test::Unit::TestCase
       q.clean
 
       q.join
-
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.1
+  version: 5.13.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-26 00:00:00.000000000 Z
+date: 2014-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake