rbbt-util 5.7.0 → 5.8.0

data/test/rbbt/annotations/test_util.rb

@@ -0,0 +1,14 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/annotations'
+
+class TestClass < Test::Unit::TestCase
+  def test_marshal
+    a = "STRING"
+    a.extend Annotated
+
+    assert_equal a, Marshal.load(Marshal.dump(a))
+    assert_equal Marshal.dump("STRING"), Marshal.dump(a)
+
+  end
+end
+

data/test/rbbt/tsv/test_parallel.rb

@@ -4,17 +4,39 @@ require 'rbbt/tsv/parallel'
 
 class TestTSVParallel < Test::Unit::TestCase
 
-  def test_pthrough
+  def _test_pthrough
     require 'rbbt/sources/organism'
-    tsv = Organism.identifiers("Hsa").tsv :unnamed => true
+    tsv = Organism.identifiers("Hsa").tsv :unnamed => true, :persist => false, :fields => ["Associated Gene Name"]
 
     h = {}
     tsv.monitor = true
+    tsv.unnamed = true
     tsv.pthrough do |k,v|
       h[k] = v.first
     end
 
-    assert h.size > 0
+    assert_equal tsv.size, h.size
+    assert_equal tsv.keys.sort, h.keys.sort
   end
 
+
+  def test_ppthrough
+    require 'rbbt/sources/organism'
+    tsv = Organism.identifiers("Hsa").tsv :unnamed => true, :persist => false, :fields => ["Associated Gene Name"]
+
+    h = {}
+
+    tsv.ppthrough_callback do |k,v|
+      h[k] = v
+    end
+
+    tsv.unnamed = true
+    tsv.monitor = true
+    tsv.ppthrough(3) do |k,v|
+      [k,v.first]
+    end
+
+    assert_equal tsv.size, h.size
+    assert_equal tsv.keys.sort, h.keys.sort
+  end
 end

data/test/rbbt/tsv/test_util.rb

@@ -23,4 +23,19 @@ row2    A    B    Id3
   
   end
 
+  def test_marshal
+   content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+
+      assert TSV === Marshal.load(Marshal.dump(tsv))
+      assert_equal tsv.to_hash, Marshal.load(Marshal.dump(tsv)).to_hash
+      assert_equal({1 => 1}, Marshal.load(Marshal.dump({1 => 1})))
+    end
+  end
 end

data/test/rbbt/util/concurrency/processes/test_socket.rb

@@ -0,0 +1,37 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../../..', 'test_helper.rb')
+
+require 'rbbt-util'
+require 'rbbt/util/log'
+require 'rbbt/util/concurrency/processes/socket'
+
+class TestConcurrency < Test::Unit::TestCase
+  def test_socket_push_pop
+    obj1 = [1,[2,3,4]] #* 1000
+    obj2 = ["1",["2","3","4"]] #* 1000
+    obj3 = "some string"
+    obj4 = TSV.setup({1 => 1})
+
+    socket = RbbtProcessQueue::RbbtProcessSocket.new 
+    10.times do
+
+      socket.push(obj1)
+      socket.push(obj2)
+      socket.push(obj3)
+      socket.push(obj4)
+
+      assert_equal obj1, socket.pop
+      assert_equal obj2, socket.pop 
+      assert_equal obj3, socket.pop 
+      assert_equal obj4, socket.pop 
+
+
+    end
+
+    socket.swrite.close
+    assert ClosedStream  === socket.pop
+
+    socket.clean
+  end
+end
+
+

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

@@ -0,0 +1,53 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+
+require 'rbbt-util'
+require 'rbbt/util/log'
+require 'rbbt/util/concurrency/processes'
+
+class TestConcurrencyProcess < Test::Unit::TestCase
+
+  def test_process
+    q = RbbtProcessQueue.new 1
+
+    res = []
+
+    q.callback do |v|
+      res << v
+    end
+
+    q.init do |i|
+      i * 2
+    end
+
+    times = 500
+    t = TSV.setup({"a" => 1}, :type => :single)
+
+    Misc.benchmark do
+    times.times do |i|
+      q.process i
+    end
+
+    q.join
+    q.clean
+    end
+
+    assert_equal times, res.length
+    assert_equal [0, 2, 4], res.sort[0..2]
+    
+  end
+
+  def test_each
+    times = 5000
+    elems = (0..times-1).to_a
+
+    TmpFile.with_file do |dir|
+      RbbtProcessQueue.each(elems) do |elem|
+        Open.write(File.join(dir, elem.to_s), "DONE")
+      end
+
+      assert_equal times, Dir.glob(File.join(dir, '*')).length
+    end
+  end
+end
+
+

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

@@ -0,0 +1,42 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/concurrency'
+
+class TestConcurrencyThreads < Test::Unit::TestCase
+  def test_thread_queue
+    q = RbbtThreadQueue.new 10
+
+    res = []
+
+    q.init do |v|
+      res << v
+    end
+
+    times = 5_000_000
+    Misc.benchmark do
+    times.times do |i|
+      q.process [i*2]
+    end
+    end
+
+    q.join
+    q.clean
+
+    assert_equal times, res.length
+    assert_equal [0, 2, 4], res.sort[0..2]
+    
+  end
+
+  def test_each
+    times = 50000
+    elems = (0..times-1).to_a
+
+    TmpFile.with_file do |dir|
+      elems.each do |elem|
+        Open.write(File.join(dir, elem.to_s), "DONE")
+      end
+
+      assert_equal times, Dir.glob(File.join(dir, '*')).length
+    end
+  end
+end
+

data/test/rbbt/util/test_concurrency.rb

@@ -0,0 +1,6 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/util/concurrency'
+
+class TestConcurrency < Test::Unit::TestCase
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.7.0
+  version: 5.8.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-03 00:00:00.000000000 Z
+date: 2014-03-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -161,6 +161,12 @@ files:
 - lib/rbbt/util/cmd.rb
 - lib/rbbt/util/color.rb
 - lib/rbbt/util/colorize.rb
+- lib/rbbt/util/concurrency.rb
+- lib/rbbt/util/concurrency/processes.rb
+- lib/rbbt/util/concurrency/processes/socket.rb
+- lib/rbbt/util/concurrency/processes/socket_old.rb
+- lib/rbbt/util/concurrency/processes/worker.rb
+- lib/rbbt/util/concurrency/threads.rb
 - lib/rbbt/util/excel2tsv.rb
 - lib/rbbt/util/filecache.rb
 - lib/rbbt/util/log.rb
@@ -193,6 +199,8 @@ files:
 - share/rbbt_commands/app/install
 - share/rbbt_commands/app/start
 - share/rbbt_commands/app/template
+- share/rbbt_commands/benchmark/pthrough
+- share/rbbt_commands/color
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list
 - share/rbbt_commands/conf/web_user/remove
@@ -203,6 +211,7 @@ files:
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get
 - share/rbbt_commands/resource/produce
+- share/rbbt_commands/stat/density
 - share/rbbt_commands/study/task
 - share/rbbt_commands/system/purge
 - share/rbbt_commands/system/report
@@ -211,6 +220,8 @@ files:
 - share/rbbt_commands/tsv/get
 - share/rbbt_commands/tsv/info
 - share/rbbt_commands/tsv/json
+- share/rbbt_commands/tsv/slice
+- share/rbbt_commands/tsv/subset
 - share/rbbt_commands/tsv/unzip
 - share/rbbt_commands/tsv/values
 - share/rbbt_commands/workflow/cmd
@@ -226,6 +237,7 @@ files:
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - share/unicorn.rb
+- test/rbbt/annotations/test_util.rb
 - test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
 - test/rbbt/persist/test_tsv.rb
@@ -253,6 +265,9 @@ files:
 - test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_parallel.rb
 - test/rbbt/tsv/test_util.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
 - test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/util/simpleopt/test_setup.rb
@@ -260,6 +275,7 @@ files:
 - test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_cmd.rb
 - test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_log.rb
@@ -307,11 +323,15 @@ test_files:
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_log.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_colorize.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
 - test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_tmpfile.rb
@@ -319,6 +339,7 @@ test_files:
 - test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
 - test/rbbt/test_knowledge_base.rb
+- test/rbbt/annotations/test_util.rb
 - test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
 - test/rbbt/test_tsv.rb