rbbt-util 5.43.0 → 5.44.1

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

@@ -1,192 +0,0 @@
-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 setup
-    #Log.severity = 0
-  end
-
-  def test_process_throttle
-    q = RbbtProcessQueue.new 10
-
-    times = 500
-
-    res = []
-    q.callback do |v|
-      res << v
-    end
-
-    q.init do |i|
-      sleep 0.001
-      Process.pid
-    end
-
-    times.times do |i|
-      q.process i
-    end
-
-    sleep 1 while res.length < times
-    assert_equal 10, res.uniq.length
-
-    q.add_process
-    sleep 0.1
-    q.add_process
-    sleep 0.1
-    q.add_process
-    sleep 0.1
-
-    times.times do |i|
-      q.process i
-    end
-
-    sleep 1 while res.length < times * 2
-    assert_equal 13, res[(times + 20)..-1].uniq.length
-
-    q.remove_process
-    sleep 0.1
-    q.remove_process
-    sleep 0.1
-    q.remove_process
-    sleep 0.1
-    q.remove_process
-    sleep 0.1
-    q.remove_process
-    sleep 0.1
-
-    times.times do |i|
-      q.process i
-    end
-
-    sleep 1 while res.length < times * 3
-    assert_equal 8, res[(2*times + 30)..-1].uniq.length
-
-    q.join
-    assert_equal times * 3, res.length
-  end
-
-  def test_process
-    q = RbbtProcessQueue.new 10
-
-    res = []
-
-    q.callback do |v|
-      res << v
-    end
-
-    q.init do |i|
-      i * 2
-    end
-
-    times = 500
-
-    times.times do |i|
-      q.process i
-    end
-
-    q.join
-
-    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
-
-  def test_error
-    assert_raise RbbtException do
-      q = RbbtProcessQueue.new 3
-
-      res = []
-
-      q.callback do |v|
-        res << v
-      end
-
-      q.init do |i|
-        raise RbbtException.new "MY ERROR" if i == 300
-        i * 2
-      end
-
-      times = 500
-
-      times.times do |i|
-        q.process i
-      end
-
-      q.join
-
-      assert_equal times, res.length
-      assert_equal [0, 2, 4], res.sort[0..2]
-    end
-  end
-
-  def test_process_abort
-    assert_raise Aborted do
-      q = RbbtProcessQueue.new 10
-
-      res = []
-
-      q.callback do |v|
-        res << v
-      end
-
-      q.init do |i|
-        sleep 1 while true
-      end
-
-      times = 500
-
-      times.times do |i|
-        q.process i
-      end
-
-      sleep 1
-      q.clean
-      sleep 1
-
-      q.join
-    end
-  end
-
-
-  def test_process_respawn
-    q = RbbtProcessQueue.new 2, nil, nil, true
-
-    res = []
-
-    q.callback do |v|
-      res << v
-    end
-
-    q.init do |i|
-      $str ||="-"
-      $str = $str *  (2 + rand(5).to_i)
-      sleep 0.1
-      "."
-    end
-
-    times = 50
-
-    times.times do |i|
-      q.process i
-    end
-
-    q.join
-  end
-end
-
-

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

@@ -1,40 +0,0 @@
-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 = 1_000_000
-    times.times do |i|
-      q.process [i*2]
-    end
-
-    q.join
-    q.clean
-
-    assert_equal times, res.length
-    assert_equal [0, 2, 4], res.sort[0..2]
-    
-  end
-
-  def test_each
-    times = 10000
-    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/log/test_progress.rb

@@ -1,111 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/log/progress'
-
-class TestProgress < Test::Unit::TestCase
-  def test_bar
-    t1 = Thread.new do
-      Log::ProgressBar.with_bar(20, :desc => "Bar 1") do |bar|
-        20.times do
-          bar.tick
-          sleep 0.3
-        end
-        Log.debug "Done progress"
-        assert_equal 100, bar.percent
-      end
-    end
-
-    t2 = Thread.new do
-      Log::ProgressBar.with_bar(20, :desc => "Bar 2") do |bar|
-        20.times do
-          bar.tick
-          sleep 0.2
-        end
-        Log.debug "Done progress"
-        assert_equal 100, bar.percent
-      end
-    end
-    t1.join
-    t2.join
-  end
-
-  def test_bar_no_size
-    t1 = Thread.new do
-      Log::ProgressBar.with_bar(nil, :desc => "Bar 1") do |bar|
-        20.times do
-          bar.tick
-          sleep 0.3
-        end
-        #Log.debug "Done progress"
-        assert bar.history.length > 0
-      end
-    end
-
-    t2 = Thread.new do
-      Log::ProgressBar.with_bar(nil, :desc => "Bar 2") do |bar|
-        20.times do
-          bar.tick
-          sleep 0.2
-        end
-        #Log.debug "Done progress"
-        assert bar.history.length > 0
-      end
-    end
-    t1.join
-    t2.join
-  end
-
-  def test_bar_nested
-    Log::ProgressBar.with_bar(20, :desc => "Bar 1") do |bar|
-      bar.init
-      20.times do
-        Log::ProgressBar.with_bar(5, :desc => "Bar 2") do |bar|
-          5.times do
-            bar.tick
-            sleep 0.2
-          end
-        end
-        bar.tick
-        sleep 0.2
-      end
-    end
-  end
-
-  def test_pos
-    size = 10000
-
-    Log::ProgressBar.with_bar(size, :desc => "Bar 1") do |bar|
-      bar.init
-      nums = []
-      100.times do
-        nums << rand(size)
-      end
-      nums.sort.each do |num|
-        bar.pos num
-        sleep 0.1
-      end
-      bar.tick
-    end
-  end
-
-  def test_file
-    size = 10000
-
-    TmpFile.with_file do |file|
-
-      Log::ProgressBar.with_bar(size, :desc => "Bar 1", :file => file) do |bar|
-        bar.init
-        nums = []
-        100.times do
-          nums << rand(size)
-        end
-        nums.sort.each do |num|
-          bar.pos num
-          sleep 0.1
-        end
-        bar.tick
-      end
-    end
-  end
-
-end
-

data/test/rbbt/util/misc/test_bgzf.rb

@@ -1,48 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/bgzf'
-
-class TestBgzf < Test::Unit::TestCase
-  def test_Bgzf
-    content = "1234567890" * 1000000
-    TmpFile.with_file(content) do |file|
-      compressed = file + '.gz'
-      `bgzip #{file} -c > #{compressed}`
-      stream = Bgzf.setup Open.open(compressed, :noz => true)
-      assert_equal "1234", stream.read(4)
-      assert_equal "56", stream.read(2)
-      stream.seek 500003
-      assert_equal "4567", stream.read(4)
-      assert_equal "89", stream.read(2)
-    end
-  end
-
-  def test_tsv
-    require 'rbbt/tsv'
-    TmpFile.with_file(datafile_test(:identifiers).read) do |file|
-      Misc.benchmark do
-        tsv = TSV.open(Open.open(file))
-      end
-
-      `gzip #{file}`
-      stream = Open.open(file + '.gz')
-      Misc.benchmark do
-        tsv = TSV.open(stream)
-      end
-
-      `gunzip #{file}.gz`
-      compressed = file + '.bgz'
-      `bgzip #{file} -c > #{compressed}`
-      stream = Bgzf.setup File.open(compressed)
-      Misc.benchmark do
-        tsv = TSV.open(stream)
-      end
-
-    end
-  end
-
-  def test_bgzip
-    assert File.exist?(Bgzf.bgzip_cmd)
-    assert 'bgzip', File.basename(Bgzf.bgzip_cmd)
-  end
-end
-

data/test/rbbt/util/misc/test_communication.rb

@@ -1,13 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/communication'
-
-class TestCommunication < Test::Unit::TestCase
-  def test_send_email
-    keyword_test :mail do
-      to = from = 'mvazque2@localhost'
-      subject = message = "Test"
-      Misc.send_email(to, from, subject, message)
-    end
-  end
-end
-

data/test/rbbt/util/misc/test_development.rb

@@ -1,26 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/development'
-
-class TestMiscDevelopment < Test::Unit::TestCase
-  def test_mem
-    assert Integer === Misc.memory_use
-  end
-
-  def ___test_ssh
-    Misc.ssh_run 'mn1' do
-      puts "hola"
-    end
-  end
-
-  def __test_timeout
-    Misc.timeout_insist(2) do
-      puts "Start"
-      3.times do
-        puts "ping"
-        sleep rand(4)
-        puts "pong"
-      end
-    end
-  end
-end
-

data/test/rbbt/util/misc/test_format.rb

@@ -1,10 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/format'
-
-class TestClass < Test::Unit::TestCase
-  def test_fixutf8
-    a = "Camión"
-    assert_equal a, Misc.fixutf8(a)
-  end
-end
-

data/test/rbbt/util/misc/test_indiferent_hash.rb

@@ -1,14 +0,0 @@
-require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
-require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
-
-class TestIndiferentHash < Test::Unit::TestCase
-  def test_recursive
-    a = {:a => {:b => 1 } }
-    IndiferentHash.setup(a)
-
-    assert IndiferentHash === a["a"]
-    assert_equal 1, a[:a]["b"]
-    assert_equal 1, a["a"][:b]
-  end
-end
-

data/test/rbbt/util/misc/test_lock.rb

@@ -1,77 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-
-require 'rbbt-util'
-require 'rbbt/util/misc/lock'
-require 'rbbt/workflow'
-
-class TestLock < Test::Unit::TestCase
-  def __test_stress
-  end
-end
-
-if __FILE__ == $0
-  def deleted(pid = Process.pid)
-    begin
-      txt = `ls -la /proc/#{pid}/fd |grep deleted`
-      puts Log.color(:magenta, [pid, txt.split("\n")*", "] * ": ")
-    rescue Exception
-      Log.exception $!
-    end
-  end
-
-  cpus = 10
-  file = "/tmp/test.lock"
-
-  pids = []
-  cpus.times do 
-    pids << Process.fork do
-      while true do
-        Lockfile.new file do
-          Lockfile.new file + '.1' do
-          end
-          File.open(file){|f| puts f.read }
-        end
-        deleted
-      end
-    end
-  end
-
-
-
-  exit
-  size = 1000000
-  num = 1
-  cpus = 5
-
-  pdb = "http://interactome3d.irbbarcelona.org/pdb.php?dataset=human&type1=interactions&type2=pdb&pdb=Q99685-Q99685-EXP-3hju.pdb1-B-0-A-0.pdb"
-  Workflow.require_workflow "Structure"
-  TmpFile.with_file do |dir|
-    Structure.workdir = dir
-    Path.setup dir
-    TSV.traverse (0..size).to_a, :cpus => cpus, :type => :array, :bar => true do |i|
-      begin
-        v = rand(num).to_s
-        file = File.join(dir, "file-" << v.to_s)
-
-        Misc.lock file + '.produce' do
-          Misc.lock file  do
-          ##job = Structure.job(:neighbour_map, v, :pdb => pdb)
-          #job = Translation.example_step(:translate, "Example")
-          #job.path = file
-          #if job.done?
-          #  job.clean if rand < 0.3
-          #else
-          #  job.run(true) 
-          #end
-          end
-        end
-        deleted Process.pid
-
-      rescue Exception
-        raise $!
-      end
-    end
-  end
-end
-
-