rbbt-util 5.22.5 → 5.23.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1c617d4a4ffaed12ddf8a5cdf44a4ff5113e47d0
-  data.tar.gz: 74125cd2876fff8d7c097d89eee4adb47f61a26c
+  metadata.gz: b7397119676c0da57371a52797ef8a3f4dc2bc0a
+  data.tar.gz: 973e8a7c4e2cb6eb960ed2b7c782dae0a615c0ac
 SHA512:
-  metadata.gz: 81bf1cb9b56203f6ab747ef961fc920146e07b78e2a220fdf2e9174adfd0effbf01974e4560ff6759c2e180d4ce03ea6c2db4fc2a047e07162c342a265735b8f
-  data.tar.gz: c4ef6e26f7683f2365f9ca15cfc045cf69a04a174d2f59a0dce0a22ede010b22f962d17d9bc03f73469338c1c47c2c6cf33a6d65173e387e6f71c633462fabfc
+  metadata.gz: 26497c36b05b98961b845562930dceb399c720ab399c5a71c16ccbefb6e5b9756c407ca4fd1ca5b679ef1fca5ea1c989fd1cd4b28b33d8ae983d82cdcfa99aa8
+  data.tar.gz: 37a2aa35faac67658a57ef32d2ab662968a4a11ba44a6a1174d79cdfd86a4315f8ee2b57b3f870b928a4e7b1138ceb5f81f12b513beff95bf00171839083bc9b

data/lib/rbbt/resource/path.rb

@@ -227,12 +227,12 @@ module Path
       compact.select{|file| file.exists? }.uniq
   end
 
-  def glob_all(caller_lib = nil, search_paths = nil)
+  def glob_all(pattern = nil, caller_lib = nil, search_paths = nil)
     search_paths ||= @search_paths || SEARCH_PATHS
     search_paths = search_paths.dup
 
     search_paths.keys.
-      collect{|where| Dir.glob(find(where, Path.caller_lib_dir, search_paths))}.
+      collect{|where| pattern ? Dir.glob(File.join(find(where, Path.caller_lib_dir, search_paths), pattern)) : Dir.glob(find(where, Path.caller_lib_dir, search_paths)) }.
       compact.flatten.collect{|file| File.expand_path(file)}.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
   end
   #{{{ Methods

data/lib/rbbt/tsv/util.rb

@@ -128,7 +128,7 @@ module TSV
           file.join
           raise "Aborted stream from Step #{file.path}" if file.aborted?
           raise "Exception in stream from Step #{file.path}: #{file.messages.last}" if file.error?
-          get_stream(file.path)
+          get_stream(file.path, open_options)
         end
       end
     when Array

data/lib/rbbt/util/cmd.rb

@@ -65,10 +65,8 @@ module CMD
 
         if IO === in_content
           in_content.close if in_content.respond_to?(:close) and not in_content.closed?
-          in_content.join if in_content.respond_to?(:join) and not in_content.joined?
         end
 
-
         STDERR.reopen serr.last
         serr.last.close
 

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

@@ -15,6 +15,10 @@ class RbbtProcessQueue
     @process_mutex = Mutex.new
   end
 
+
+  ABORT_SIGNAL = :INT
+  CLOSE_SIGNAL = :PIPE
+
   attr_accessor :callback, :callback_queue, :callback_thread
   def callback(&block)
     if block_given?
@@ -64,8 +68,9 @@ class RbbtProcessQueue
 
     @master_pid = Process.fork do
       @close_up = false
-      Signal.trap(:INT) do
-        @close_up = true
+
+      Signal.trap(CLOSE_SIGNAL) do
+        @close_up = true unless @closing_thread
         Misc.insist([0,0.01,0.1,0.2,0.5]) do
           raise TryAgain unless @manager_thread
           if @manager_thread.alive?
@@ -75,6 +80,25 @@ class RbbtProcessQueue
         end
       end
 
+      Signal.trap(:USR1) do
+        @count += 1
+        @manager_thread.raise TryAgain
+      end
+
+      Signal.trap(:USR2) do
+        @count -= 1
+        @manager_thread.raise TryAgain
+      end
+
+      Signal.trap(ABORT_SIGNAL) do
+        begin
+          @monitor_thread.raise Aborted
+        rescue Exception
+          Log.exception $!
+        end
+      end
+
+
       if @callback_queue
         Misc.purge_pipes(@queue.swrite,@queue.sread,@callback_queue.swrite, @callback_queue.sread) 
       else
@@ -91,15 +115,16 @@ class RbbtProcessQueue
           begin
             Thread.current["working"] = true
             if @close_up
+              @close_up = false
               Log.debug "Closing up process queue #{Process.pid}"
               @count = 0
-              Thread.new do
+              @closing_thread = Thread.new do
                 Log.debug "Pushing closed stream #{Process.pid}"
                 while true
                   @queue.push ClosedStream.new unless @queue.cleaned 
+                  break if @processes.empty?
                 end unless @processes.empty?
               end
-              @close_up = false
             end
 
             begin
@@ -141,17 +166,6 @@ class RbbtProcessQueue
         end
       end
 
-      Signal.trap(:USR1) do
-        @count += 1
-        @manager_thread.raise TryAgain
-      end
-
-      Signal.trap(:USR2) do
-        @count -= 1
-        @manager_thread.raise TryAgain
-      end
-
-
       @callback_queue.close_read if @callback_queue
 
       num_processes.times do |i|
@@ -183,16 +197,12 @@ class RbbtProcessQueue
         end
       end
 
-      Signal.trap(20) do
-        begin
-          @monitor_thread.raise Aborted.new
-        rescue Exception
-          Log.exception $!
-        end
-      end
 
       begin
-        @monitor_thread.join
+
+        while @monitor_thread.alive?
+          @monitor_thread.join(1)
+        end
       rescue Exception
         Log.exception $!
       end
@@ -222,7 +232,7 @@ class RbbtProcessQueue
     rescue Exception
       Log.warn "Error closing callback: #{$!.message}"
     end
-    @callback_thread.join  #if @callback_thread.alive?
+    @callback_thread.join  if @callback_thread && @callback_thread.alive?
     t.join
   end
 
@@ -240,6 +250,8 @@ class RbbtProcessQueue
       Log.error "Exception joining queue: #{$!.message}"
       raise $!
     ensure
+      close_callback if @callback
+      @callback_thread.join if @callback_thread
       if @join
         if @join.arity == 1
           @join.call(error) 
@@ -253,7 +265,7 @@ class RbbtProcessQueue
 
   def join
     begin
-      Process.kill :INT, @master_pid
+      Process.kill CLOSE_SIGNAL, @master_pid
     rescue Errno::ECHILD, Errno::ESRCH
       Log.debug "Cannot kill #{@master_pid}: #{$!.message}"
     end 
@@ -264,20 +276,16 @@ class RbbtProcessQueue
       close_callback if @callback
       @queue.swrite.close unless @queue.swrite.closed?
     end
-    @callback_thread.join if @callback_thread
+    #@callback_thread.join if @callback_thread
     self.clean
   end
 
   def _abort
     begin
-      Process.kill 20, @master_pid
+      Process.kill ABORT_SIGNAL, @master_pid
+      pid, status = Process.waitpid2 @master_pid
     rescue Errno::ECHILD, Errno::ESRCH
-      Log.debug "Cannot kill #{@master_pid}: #{$!.message}"
-    end
-
-    begin
-      _join
-    rescue ProcessFailed
+      Log.warn "Cannot kill #{@master_pid}: #{$!.message}"
     end
   end
 

data/lib/rbbt/util/log/progress.rb

@@ -61,5 +61,10 @@ module Log
         Log.exception $!
       end
     end
+
+    def pos(pos)
+      step = pos - (@ticks || 0)
+      tick(step)
+    end
   end
 end

data/lib/rbbt/util/misc/concurrent_stream.rb

@@ -18,10 +18,10 @@ module ConcurrentStream
     stream.pids ||= []
     stream.threads.concat(Array === threads ? threads : [threads]) unless threads.nil? 
     stream.pids.concat(Array === pids ? pids : [pids]) unless pids.nil? or pids.empty?
-    stream.autojoin = autojoin
-    stream.no_fail = no_fail
+    stream.autojoin = autojoin unless autojoin.nil?
+    stream.no_fail = no_fail unless no_fail.nil?
 
-    stream.pair = pair if pair
+    stream.pair = pair unless pair.nil?
 
     callback = block if block_given?
     if callback
@@ -50,7 +50,7 @@ module ConcurrentStream
 
     stream.filename = filename unless filename.nil?
 
-    stream.lockfile = lockfile if lockfile
+    stream.lockfile = lockfile unless lockfile.nil?
 
     stream.aborted = false
 
@@ -219,4 +219,12 @@ module ConcurrentStream
     end
   end
 
+  def raise(exception)
+    threads.each do |thread|
+      thread.raise exception
+    end
+
+    self.abort
+  end
+
 end

data/lib/rbbt/util/misc/omics.rb

@@ -266,9 +266,9 @@ module Misc
   end
 
 
-  def self.sort_mutations(mutations)
+  def self.sort_mutations_strict(mutations)
     mutations.collect do |mutation|
-      chr,pos,mut = mutation.split ":"
+      chr, pos, mut = mutation.split ":"
       chr.sub!(/^chr/i,'')
       chr = 22 if chr == "Y"
       chr = 23 if chr == "X"
@@ -293,6 +293,10 @@ module Misc
     end.collect{|p| p.last }
   end
 
+  class << self
+    alias sort_mutations sort_mutations_strict 
+  end
+
   def self.ensembl_server(organism)
     date = organism.split("/")[1]
     if date.nil?
@@ -302,8 +306,12 @@ module Misc
     end
   end
 
+  def self.sort_genomic_locations_strict(stream, sep = ":")
+    sort_stream(stream, '#', "-k1,1V -k2,2n -t#{sep}")
+  end
+  
   def self.sort_genomic_locations(stream)
-    sort_stream(stream, '#', '-k1,1 -k2,2n -t:')
+    sort_stream(stream, '#', "-k1,1 -k2,2n -t#{sep}")
   end
 
   def self.intersect_streams_read(io, sep=":")
@@ -319,18 +327,46 @@ module Misc
     [line,chr, start, eend, rest]
   end
 
-  def self.intersect_streams_cmp_chr(chr1, chr2)
-    if chr1 =~ /^\d+$/ and chr2 =~ /^\d+$/
-      chr1 <=> chr2
-    elsif chr1 =~ /^\d+$/
+  def self.chr_cmp_strict(chr1, chr2)
+    if (m1 = chr1.match(/(\d+)$/)) && (m2 = chr2.match(/(\d+)$/))
+      m1[1].to_i <=> m2[1].to_i
+    elsif chr1 =~ /\d+$/
       -1
-    elsif chr2 =~ /^\d+$/
+    elsif chr2 =~ /\d+$/
       1
     else
       chr1 <=> chr2
     end
   end
 
+  def self.genomic_location_cmp(gpos1, gpos2, sep = ":")
+    chr1, _sep, pos1 = gpos1.partition(sep)
+    chr2, _sep, pos2 = gpos2.partition(sep)
+    cmp = chr1 <=> chr2
+    case cmp
+    when 0
+      pos1.to_i <=> pos2.to_i
+    else
+      cmp
+    end
+  end
+
+  def self.genomic_location_cmp_strict(gpos1, gpos2, sep = ":")
+    chr1, _sep, pos1 = gpos1.partition(sep)
+    chr2, _sep, pos2 = gpos2.partition(sep)
+    cmp = chr_cmp_strict(chr1, chr2)
+    case cmp
+    when 0
+      pos1.to_i <=> pos2.to_i
+    else
+      cmp
+    end
+  end
+
+  def self.intersect_streams_cmp_chr(chr1, chr2)
+    chr1 <=> chr2
+  end
+
   def self.intersect_streams(f1, f2, out, sep=":")
     finish = false
     return if f1.eof? or f2.eof?
@@ -404,7 +440,7 @@ module Misc
       max_size = 0
       nio = Misc.open_pipe do |sin|
         while line = io.gets
-          chr, start, eend, id, *rest = line.split("\t")
+          chr, start, eend, id, *rest = line.chomp.split("\t")
           l = id.length
           max_size = l if max_size < l
           chr = chr.sub('chr','')
@@ -422,6 +458,7 @@ module Misc
         end
 
         TSV.traverse tmpfile, :type => :array, :bar => "Creating BED index for #{Misc.fingerprint source}" do |line|
+          next if line.empty?
           chr, start, eend, id, *rest = line.split("\t")
           key = [chr, start, eend] * ":"
           sharder[key] = id

data/lib/rbbt/util/misc/pipes.rb

@@ -197,7 +197,10 @@ module Misc
         rescue IOError
         end
 
+        stream.close unless stream.closed?
+        stream.join if stream.respond_to? :join
         in_pipes.first.close
+        #Log.medium "Tee done #{Misc.fingerprint stream}"
       rescue Aborted, Interrupt
         stream.abort if stream.respond_to? :abort
         out_pipes.each do |sout|
@@ -219,10 +222,11 @@ module Misc
       ConcurrentStream.setup sout, :threads => splitter_thread, :filename => filename, :_pair => stream
     end
 
-    out_pipes.first.autojoin = true
+    main_pipe = out_pipes.first
+    main_pipe.autojoin = true
 
-    out_pipes.first.callback = Proc.new do 
-      stream.join
+    main_pipe.callback = Proc.new do 
+      stream.join if stream.respond_to? :join
       in_pipes[1..-1].each do |sin|
         sin.close unless sin.closed?
       end
@@ -246,7 +250,7 @@ module Misc
     rest
   end
 
-  def Misc.dup_stream (stream)
+  def self.dup_stream(stream)
     dup_stream_multiple(stream, 1).first
   end
 
@@ -314,6 +318,8 @@ module Misc
         into.close if into and into_close and not into.closed?
         into.join if into and into_close and into.respond_to?(:joined?) and not into.joined?
         block.call if block_given?
+
+        #Log.medium "Done consuming stream #{Misc.fingerprint io}"
       rescue Aborted
         Log.medium "Consume stream aborted #{Misc.fingerprint io}"
         io.abort if io.respond_to? :abort
@@ -514,7 +520,7 @@ module Misc
     end
   end
 
-  def self._paste_streams(streams, output, lines = nil, sep = "\t", header = nil)
+  def self._paste_streams(streams, output, lines = nil, sep = "\t", header = nil, &block)
     output.puts header if header
     streams = streams.collect do |stream|
       if defined? Step and Step === stream
@@ -542,7 +548,11 @@ module Misc
       sizes = parts.collect{|p| p.nil? ? 0 : p.length }
       last_min = nil
       while lines.compact.any?
-        min = keys.compact.sort.first
+        if block_given?
+          min = keys.compact.sort(&block).first
+        else
+          min = keys.compact.sort.first
+        end
         str = []
         keys.each_with_index do |key,i|
           case key
@@ -576,11 +586,11 @@ module Misc
     end
   end
 
-  def self.paste_streams(streams, lines = nil, sep = "\t", header = nil)
+  def self.paste_streams(streams, lines = nil, sep = "\t", header = nil, &block)
     sep ||= "\t"
     num_streams = streams.length
     Misc.open_pipe do |sin|
-      self._paste_streams(streams, sin, lines, sep, header)
+      self._paste_streams(streams, sin, lines, sep, header, &block)
     end
   end
 
@@ -667,11 +677,14 @@ module Misc
     end
   end
 
+  def self.sort_mutation_stream_strict(stream, sep=":")
+    CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -V -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
+  end
+
   def self.sort_mutation_stream(stream, sep=":")
     CMD.cmd("grep '#{sep}' | sort -u | sed 's/^M:/MT:/' | env LC_ALL=C sort -k1,1 -k2,2n -k3,3n -t'#{sep}'", :in => stream, :pipe => true, :no_fail => true)
   end
 
-
   def self.swap_quoted_character(stream, charout="\n", charin=" ", quote='"')
     io = Misc.open_pipe do |sin|
       begin
@@ -698,4 +711,27 @@ module Misc
     swap_quoted_character(stream, "\n", " ", quote)
   end
 
+  def self.line_monitor_stream(stream, &block)
+    monitor, out = tee_stream stream
+    monitor_thread = Thread.new do
+      begin
+        while line = monitor.gets
+          block.call line
+        end
+      rescue
+        Log.exception $!
+        monitor.raise $!
+        monitor.close unless monitor.closed?
+        monitor.join if monitor.respond_to?(:join) && ! monitor.aborted?
+        out.raise $! if out.respond_to?(:raise)
+      ensure
+        monitor.close unless monitor.closed?
+        monitor.join if monitor.respond_to?(:join) && ! monitor.aborted?
+      end
+    end
+
+    stream.annotate out if stream.respond_to? :annotate
+    ConcurrentStream.setup out, :threads => monitor_thread
+  end
+
 end

data/lib/rbbt/util/open.rb

@@ -236,6 +236,13 @@ module Open
     end
   end
 
+  def self.mkdir(target)
+    target = target.find if Path === target
+    if not File.exists?(target)
+      FileUtils.mkdir_p target
+    end
+  end
+
   def self.ln_s(source, target, options = {})
     source = source.find if Path === source
     target = target.find if Path === target
@@ -346,6 +353,14 @@ module Open
     CMD.cmd('zcat', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
   end
 
+  def self.gzip(stream)
+    CMD.cmd('gzip', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
+  end
+
+  def self.bgzip(stream)
+    CMD.cmd('bgzip', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
+  end
+
   def self.unzip(stream)
     TmpFile.with_file(stream.read) do |filename|
       StringIO.new(CMD.cmd("unzip '{opt}' #{filename}", "-p" => true, :pipe => true).read)

data/lib/rbbt/workflow.rb

@@ -299,7 +299,6 @@ module Workflow
     taskname = taskname.to_sym
     return remote_tasks[taskname].job(taskname, jobname, inputs) if remote_tasks and remote_tasks.include? taskname
 
-    jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?
 
     task = tasks[taskname]
     raise "Task not found: #{ taskname }" if task.nil?
@@ -326,7 +325,15 @@ module Workflow
       raise ParameterException, "Inputs #{Misc.humanize_list(missing_inputs)} are required but were not provided or are nil"
     end
 
-    dependencies = real_dependencies(task, jobname, defaults.merge(inputs), task_dependencies[taskname] || [])
+    if task.input_options
+      jobname_input = task.input_options.select{|i,o| o[:jobname]}.collect{|i,o| i }.first
+    else
+      jobname_input = nil 
+    end
+
+    if jobname_input && jobname && inputs[jobname_input].nil?
+      inputs[jobname_input] = jobname
+    end
 
     real_inputs = {}
 
@@ -339,6 +346,14 @@ module Workflow
       real_inputs[k] = v 
     end
 
+    jobname_input_value = inputs[jobname_input] || defaults[jobname_input]
+    if jobname_input && jobname.nil? && String === jobname_input_value && ! jobname_input_value.include?('/')
+      jobname = jobname_input_value
+    end
+
+    jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?
+
+    dependencies = real_dependencies(task, jobname, defaults.merge(inputs), task_dependencies[taskname] || [])
     overriden = dependencies.select{|dep| dep.overriden }.any?
 
     if real_inputs.empty? and not Workflow::TAG == :inputs and not overriden 

data/lib/rbbt/workflow/accessor.rb

@@ -325,12 +325,14 @@ class Step
 
   def exception(ex, msg = nil)
     ex_class = ex.class.to_s
-    set_info :backtrace, ex.backtrace
-    set_info :exception, {:class => ex_class, :message => ex.message, :backtrace => ex.backtrace}
+    backtrace = ex.backtrace if ex.respond_to?(:backtrace)
+    message = ex.message if ex.respond_to?(:message)
+    set_info :backtrace, backtrace
+    set_info :exception, {:class => ex_class, :message => message, :backtrace => backtrace}
     if msg.nil?
-      log :error, "#{ex_class} -- #{ex.message}"
+      log :error, "#{ex_class} -- #{message}"
     else
-      log :error, "#{msg} -- #{ex.message}"
+      log :error, "#{msg} -- #{message}"
     end
     self._abort
   end
@@ -575,6 +577,53 @@ class Step
     end
   end
 
+  def monitor_stream(stream, options = {}, &block)
+    case options[:bar] 
+    when TrueClass
+      bar = progress_bar 
+    when Hash
+      bar = progress_bar options[:bar]
+    when Numeric
+      bar = progress_bar :max => options[:bar]
+    else
+      bar = options[:bar]
+    end
+
+    out = if bar.nil?
+            Misc.line_monitor_stream stream, &block
+          elsif (block.nil? || block.arity == 0)
+            Misc.line_monitor_stream stream do
+              bar.tick
+            end
+          elsif block.arity == 1
+            Misc.line_monitor_stream stream do |line|
+              bar.tick
+              block.call line
+            end
+          elsif block.arity == 2
+            Misc.line_monitor_stream stream do |line|
+              block.call line, bar
+            end
+          end
+
+    ConcurrentStream.setup(out, :abort_callback => Proc.new{
+      Log::ProgressBar.remove_bar(bar, true) if bar
+    }, :callback => Proc.new{
+      Log::ProgressBar.remove_bar(bar) if bar
+    })
+
+    bgzip = (options[:compress] || options[:gzip]).to_s == 'bgzip'
+    bgzip = true if options[:bgzip]
+
+    gzip = true if options[:compress] || options[:gzip]
+    if bgzip
+      Open.bgzip(out)
+    elsif gzip
+      Open.gzip(out)
+    else
+      out
+    end
+  end
 end
 
 module Workflow
@@ -1040,4 +1089,5 @@ module Workflow
     [exec_exports, synchronous_exports, asynchronous_exports, stream_exports].compact.flatten.uniq
   end
 
+
 end

data/lib/rbbt/workflow/step/run.rb

@@ -354,7 +354,7 @@ class Step
             ConcurrentStream.setup stream, :callback => callback, :abort_callback => abort_callback
 
             if AbortedStream === stream 
-              exception = stream.exception || Aborted
+              exception = stream.exception || Aborted.new("Aborted stream: #{Misc.fingerprint stream}")
               self.exception exception
               _clean_finished
               raise exception

data/share/rbbt_commands/workflow/task

@@ -281,7 +281,7 @@ end
 
 usage workflow, task and exit 0 if help
 
-name = options.delete(:jobname) || "Default"
+name = options.delete(:jobname) 
 
 # get job args
 sopt_option_string = SOPT_options(workflow, task)

data/test/rbbt/test_resource.rb

@@ -34,7 +34,6 @@ class TestTSV < Test::Unit::TestCase
   end
 
   def __test_rake
-    iii TestResource.tmp.test.work.footest.foo.find
     TestResource.tmp.test.work.footest.foo.read == "TEST"
     assert TestResource.tmp.test.work.footest.foo.read == "TEST"
   end

data/test/rbbt/test_workflow.rb

@@ -124,12 +124,27 @@ for this dependency
     step(:t1).load + step(:t2).load
   end
 
+  input :name, :string, "Name", nil, :jobname => true
+  task :call_name => :string do |name|
+    "Hi #{name}"
+  end
+
 end
 
 TestWF.workdir = Rbbt.tmp.test.workflow
 
 class TestWorkflow < Test::Unit::TestCase
 
+  def test_as_jobname
+    job = TestWF.job(:call_name, "Miguel")
+    assert_equal "Hi Miguel", job.run
+    assert_equal "Miguel", job.clean_name
+
+    job = TestWF.job(:call_name, nil, :name => "Miguel")
+    assert_equal "Hi Miguel", job.run
+    assert_equal "Miguel", job.clean_name
+  end
+
   def test_update_on_input_dependency_update
     send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
     send_input_dep_to_reverse_job.clean

data/test/rbbt/util/log/test_progress.rb

@@ -68,7 +68,23 @@ class TestProgress < Test::Unit::TestCase
         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
 
 end

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

@@ -78,7 +78,6 @@ class TestMiscOmics < Test::Unit::TestCase
       end
     end
 
-
     io = Misc.open_pipe do |sin|
       sin.write text
     end

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

@@ -131,13 +131,17 @@ row2 AA BB CC
 row3 AAA BBB CCC
 row1 A B C
     EOF
+    Log.severity = 0
 
     text = text * 10000
     TmpFile.with_file(text) do |tmp|
       io = Open.open(tmp)
       dup = Misc.dup_stream(io)
-      Misc.consume_stream io, true
-      assert_equal text, dup.read
+      new_text = StringIO.new ""
+      Misc.consume_stream dup, true, new_text
+      Misc.consume_stream io, false
+      new_text.rewind
+      assert_equal text, new_text.read
     end
 
 
@@ -244,7 +248,25 @@ line4
       out.rewind
       assert_equal text, out.read
     end
+  end
 
+  def test_monitor
+    text =<<-EOF
+line1
+line2
+line3
+line4
+    EOF
 
+    Log.severity = 0
+    TmpFile.with_file(text) do |file|
+      io = Open.open(file)
+      lines = Set.new
+      io2 = Misc.line_monitor_stream io do |line|
+        lines << line
+      end
+      Misc.consume_stream(io2, false)
+      assert_equal text, lines.to_a * ""
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.22.5
+  version: 5.23.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-17 00:00:00.000000000 Z
+date: 2018-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake