rbbt-util 5.13.2 → 5.13.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 48c8543fb121288f15a998bf4ce0237e56bdc2a8
+  metadata.gz: 715d410e93dddd02e14dd6d04f31917470c10b3d
+  data.tar.gz: 473271c8efe67c3465b204078d228618bedbc327
 SHA512:
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+  data.tar.gz: fb333f016809936f1ab2a928934683a3759a16d5ff3238e088535a7802f62566a732bfc7e7b0e3a7d638ebaa978b6dad6856ef2f3d5795f068213c5c14751e3a

data/lib/rbbt/persist.rb

@@ -202,7 +202,6 @@ module Persist
       rescue Aborted
         Log.warn "Persist stream thread aborted: #{ Log.color :blue, path }"
         file.abort if file.respond_to? :abort
-        parent.raise $!
       rescue Exception
         Log.warn "Persist stream thread exception: #{ Log.color :blue, path }"
         file.abort if file.respond_to? :abort
@@ -284,7 +283,7 @@ module Persist
         res = tee_stream(res, path, type, res.respond_to?(:callback)? res.callback : nil)
         ConcurrentStream.setup res do
           begin
-            lockfile.unlock if lockfile.locked?
+            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
           rescue
             Log.exception $!
             Log.warn "Lockfile exception: " << $!.message
@@ -292,7 +291,7 @@ module Persist
         end
         res.abort_callback = Proc.new do
           begin
-            lockfile.unlock if lockfile.locked?
+            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
           rescue
             Log.exception $!
             Log.warn "Lockfile exception: " << $!.message
@@ -303,7 +302,7 @@ module Persist
         res = tee_stream(res.stream, path, type, res.respond_to?(:callback)? res.callback : nil)
         ConcurrentStream.setup res do
           begin
-            lockfile.unlock if lockfile.locked?
+            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
           rescue
             Log.exception $!
             Log.warn "Lockfile exception: " << $!.message
@@ -311,7 +310,7 @@ module Persist
         end
         res.abort_callback = Proc.new do
           begin
-            lockfile.unlock if lockfile.locked?
+            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
           rescue
             Log.exception $!
             Log.warn "Lockfile exception: " << $!.message

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -10,7 +10,29 @@ module TSV
     end
   end
 
+  def self.guess_max(obj)
+    begin
+      case obj
+      when Step
+        if obj.done?
+          CMD.cmd("wc -l '#{obj.path.find}'").read.to_i
+        else
+          nil
+        end
+      when Array, Hash
+        obj.size
+      when File
+        CMD.cmd("wc -l '#{obj.filename}'").read.to_i
+      when Path
+        CMD.cmd("wc -l '#{obj.find}'").read.to_i
+      end
+    rescue
+      nil
+    end
+  end
+
   def self.stream_name(obj)
+    return "nil" if obj.nil?
     filename_obj   = obj.respond_to?(:filename) ? obj.filename : nil
     filename_obj ||= obj.respond_to?(:path) ? obj.path : nil
     stream_obj = obj_stream(obj) || obj
@@ -149,7 +171,6 @@ module TSV
 
     Log.medium "Traversing #{stream_name(obj)} #{Log.color :green, "->"} #{stream_name(options[:into])}"
     begin
-      sleep 1
       case obj
       when TSV
         traverse_tsv(obj, options, &block)
@@ -173,7 +194,6 @@ module TSV
           end
         rescue Aborted
           obj.abort if obj.respond_to? :abort
-          raise $!
         rescue Exception
           obj.abort if obj.respond_to? :abort
           raise $!
@@ -216,20 +236,28 @@ module TSV
       Log.warn "IOError traversing #{stream_name(obj)}: #{$!.message}"
       stream = obj_stream(obj)
       stream.abort if stream and stream.respond_to? :abort
+      stream = obj_stream(options[:into])
+      stream.abort if stream.respond_to? :abort
       raise $!
     rescue Errno::EPIPE
       Log.warn "Pipe closed while traversing #{stream_name(obj)}: #{$!.message}"
+      stream = obj_stream(obj)
+      stream.abort if stream and stream.respond_to? :abort
+      stream = obj_stream(options[:into])
+      stream.abort if stream.respond_to? :abort
       raise $!
     rescue Aborted
       Log.warn "Aborted traversing #{stream_name(obj)}"
       stream = obj_stream(obj)
       stream.abort if stream and stream.respond_to? :abort
-      raise $!
+      stream = obj_stream(options[:into])
+      stream.abort if stream.respond_to? :abort
     rescue Exception
       Log.warn "Exception traversing #{stream_name(obj)}"
-      Log.exception $!
       stream = obj_stream(obj)
       stream.abort if stream and stream.respond_to? :abort
+      stream = obj_stream(options[:into])
+      stream.abort if stream.respond_to? :abort
       raise $!
     end
   end
@@ -263,40 +291,38 @@ module TSV
   def self.traverse_cpus(num, obj, options, &block)
     begin
       callback, cleanup, join = Misc.process_options options, :callback, :cleanup, :join
-      q = RbbtProcessQueue.new num, cleanup, join
 
-      q.callback &callback
-      q.init &block
+      begin
+        q = RbbtProcessQueue.new num, cleanup, join
+        q.callback &callback
+        q.init &block
 
-      thread = Thread.new do 
         traverse_obj(obj, options) do |*p|
           q.process *p
         end
-      end
-
-      begin
-        thread.join
-      rescue 
+      rescue Aborted, Errno::EPIPE
+        Log.warn "Aborted"
+      rescue Exception
+        Log.exception $!
         raise $!
+      ensure
+        q.join
       end
     rescue Interrupt, Aborted
-      Log.warn "Aborted traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}"
+      Log.warn "Aborted traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.backtrace*","}"
+      q.abort
       stream = obj_stream(obj)
       stream.abort if stream.respond_to? :abort
       stream = obj_stream(options[:into])
       stream.abort if stream.respond_to? :abort
-      q.abort
-      raise $!
+      raise "Traversal aborted"
     rescue Exception
-      Log.warn "Exception during traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}"
+      Log.warn "Exception during traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.message}"
       stream = obj_stream(obj)
       stream.abort if stream.respond_to? :abort
       stream = obj_stream(options[:into])
       stream.abort if stream.respond_to? :abort
-      q.abort
       raise $!
-    ensure
-      q.join
     end
   end
 
@@ -326,8 +352,15 @@ module TSV
         store << value
       end 
       true
-    rescue
-      raise "Error storing into #{store.inspect}: #{$!.message}"
+    rescue Aborted, Interrupt
+      Log.warn "Aborted storing into #{Misc.fingerprint store}: #{$!.message}"
+      stream = obj_stream(store)
+      stream.abort if stream.respond_to? :abort
+    rescue Exception
+      stream = obj_stream(store)
+      stream.abort if stream.respond_to? :abort
+      Log.exception $!
+      raise $!
     end
   end
 
@@ -423,15 +456,16 @@ module TSV
 
     bar = Misc.process_options options, :bar
     bar ||= Misc.process_options options, :progress
+    max = guess_max(obj)
     options[:bar] = case bar
                     when String
-                      Log::ProgressBar.new_bar(nil, {:desc => bar}) 
+                      Log::ProgressBar.new_bar(max, {:desc => bar}) 
                     when TrueClass
-                      Log::ProgressBar.new_bar(nil, nil) 
+                      Log::ProgressBar.new_bar(max, nil) 
                     when Fixnum
                       Log::ProgressBar.new_bar(bar) 
                     when Hash
-                      max = Misc.process_options bar, :max
+                      max = Misc.process_options(bar, :max) || max
                       Log::ProgressBar.new_bar(max, bar) 
                     else
                       bar
@@ -448,10 +482,10 @@ module TSV
         begin
           store_into into, e
         rescue Aborted
-          raise $!
+          Log.warn "Aborted callback #{stream_name(obj)} #{Log.color :green, "->"} #{stream_name(options[:into])}"
         rescue Exception
+          Log.warn "Exception callback #{stream_name(obj)} #{Log.color :green, "->"} #{stream_name(options[:into])}"
           Log.exception $!
-          raise $!
         ensure
           bar.tick if bar
         end

data/lib/rbbt/tsv/parser.rb

@@ -537,12 +537,11 @@ module TSV
             break
           rescue Errno::EPIPE
             Log.error "Pipe closed while parsing #{Misc.fingerprint stream}: #{$!.message}"
+            stream.abort if stream.respond_to? :abort
             raise $!
           rescue Exception
             Log.error "Exception parsing #{Misc.fingerprint stream}: #{$!.message}"
-            Log.exception $!
             stream.abort if stream.respond_to? :abort
-            stream.join if stream.respond_to? :join
             raise $!
           end
         end

data/lib/rbbt/tsv/stream.rb

@@ -130,7 +130,7 @@ module TSV
                                 end
               if line.nil?
                 stream = streams[i]
-                #stream.join if stream.respond_to? :join
+                stream.join if stream.respond_to? :join
                 keys[i] = nil
                 parts[i] = nil
               else
@@ -146,12 +146,13 @@ module TSV
           sin.puts [min, str*sep] * sep
         end
         streams.each do |stream|
-          #stream.join if stream.respond_to? :join
+          stream.join if stream.respond_to? :join
         end
-      rescue 
-        Log.exception $!
+      rescue Exception
         streams.each do |stream|
-          stream.abort if stream.respond_to? :abort
+          Thread.new do
+            stream.abort if stream.respond_to? :abort
+          end
         end
         raise $!
       end

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

@@ -29,11 +29,14 @@ class RbbtProcessQueue
             @callback.call p
           end
         rescue Aborted
-          parent.raise $!
+          Log.warn "Callback thread aborted"
+          @process_monitor.raise Aborted.new
+          raise $!
         rescue ClosedStream
         rescue Exception
-          Log.warn "Callback thread exception"
-          parent.raise $!
+          Log.warn "Callback thread exception: #{$!.message}"
+          @process_monitor.raise $!
+          raise $!
         ensure
           @callback_queue.sread.close unless @callback_queue.sread.closed?
         end
@@ -56,14 +59,14 @@ class RbbtProcessQueue
           @processes.shift
         end
       rescue Aborted
+        Log.warn "Aborting process monitor"
         @processes.each{|p| p.abort }
         @processes.each{|p| p.join }
-        Log.warn "Process monitor aborted"
       rescue Exception
         Log.warn "Process monitor exception: #{$!.message}"
         @processes.each{|p| p.abort }
-        @callback_thread.raise $! if @callback_thread
-        parent.raise $!
+        @callback_thread.raise $! if @callback_thread and @callback_thread.alive?
+        raise $!
       end
     end
   end
@@ -71,22 +74,25 @@ class RbbtProcessQueue
   def close_callback
     begin
       @callback_queue.push ClosedStream.new if @callback_thread.alive?
-    rescue
+    rescue Exception
       Log.warn "Error closing callback: #{$!.message}"
     end
-    @callback_thread.join  if @callback_thread.alive?
+    @callback_thread.join  #if @callback_thread.alive?
   end
 
   def join
-    @processes.length.times do 
-      @queue.push ClosedStream.new
-    end if @process_monitor.alive?
+    begin
+      @processes.length.times do 
+        @queue.push ClosedStream.new
+      end if @process_monitor.alive?
+    rescue Exception
+    end
 
     begin
       @process_monitor.join
       close_callback if @callback
     rescue Exception
-      Log.exception $!
+      Log.error "Exception joining queue: #{$!.message}"
       raise $!
     ensure
       @queue.swrite.close unless @queue.swrite.closed?
@@ -113,7 +119,11 @@ class RbbtProcessQueue
   end
 
   def process(*e)
-    @queue.push e
+    begin
+      @queue.push e
+    rescue Errno::EPIPE
+      raise Aborted
+    end
   end
 
   def self.each(list, num = 3, &block)

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

@@ -35,7 +35,6 @@ class RbbtProcessQueue
           Log.warn "Worker #{Process.pid} aborted"
           Kernel.exit! -1
         rescue Exception
-          Log.exception $!
           @callback_queue.push($!) if @callback_queue
           Kernel.exit! -1
         ensure
@@ -45,10 +44,7 @@ class RbbtProcessQueue
     end
 
     def join
-      begin
-        joined_pid = Process.waitpid @pid
-      rescue
-      end
+      joined_pid = Process.waitpid @pid
     end
 
     def abort

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

@@ -103,7 +103,10 @@ module Log
     end
 
     def thr
-      @last_report = Time.now if @last_report == -1
+      if @last_report == -1
+        @last_report = Time.now 
+        return thr
+      end
       time = Time.now - @last_report
       time = 0.000001 if time == 0
       thr = (@current / time).to_i
@@ -140,6 +143,10 @@ module Log
       indicator
     end
 
+    def msg
+      @max ? report_msg : throughput_msg
+    end
+
     def print(io, str)
       LOG_MUTEX.synchronize do
         STDERR.print str
@@ -153,9 +160,9 @@ module Log
     # original line. Everything is printed to stderr.
     def report(io = STDERR)
       if Log::LAST != "progress"
-        Log::ProgressBar.cleanup_bars
-        print(io, Log.color(:yellow, "== Progress"))
-        (BARS.length-1).times{print(io, "\n")}
+        Log::LAST.replace "progress"
+        length = Log::ProgressBar.cleanup_bars
+        length.times{print(io, "\n")}
       end
       print(io, up_lines(@depth) << report_msg << down_lines(@depth)) if severity >= Log.severity
       @last_report = Time.now if @last_report == -1
@@ -163,9 +170,9 @@ module Log
 
     def throughput(io = STDERR)
       if Log::LAST != "progress"
-        Log::ProgressBar.cleanup_bars
-        print(io, Log.color(:yellow, "== Progress"))
-        (BARS.length-1).times{print(io, "\n")}
+        Log::LAST.replace "progress"
+        length = Log::ProgressBar.cleanup_bars 
+        length.times{print(io, "\n")}
       end
       print(io, up_lines(@depth) << throughput_msg << down_lines(@depth)) if severity >= Log.severity
       @last_report = Time.now
@@ -173,6 +180,11 @@ module Log
     end
 
     def done
+      if Log::LAST != "progress"
+        Log::LAST.replace "progress"
+        length = Log::ProgressBar.cleanup_bars 
+        length.times{print(io, "\n")}
+      end
       print(io, up_lines(@depth) << Log.color(:magenta, @desc) << Log.color(:green, " DONE") << down_lines(@depth)) if severity >= Log.severity
     end
 
@@ -193,22 +205,22 @@ module Log
         REMOVE.each do |bar|
           index = BARS.index bar
           if index
-            (index..BARS.length-1).each do |pos|
-              bar = BARS[pos]
-              bar.depth = pos - 1
-              BARS[pos-1] = bar
-            end 
-            BARS.pop
+            BARS.delete_at index
+            BARS.each_with_index do |bar,i|
+              bar.depth = i
+            end
           end
         end
         REMOVE.clear
+        BARS.length
       end
     end
 
     def self.remove_bar(bar)
+      bar.done unless bar.max
       BAR_MUTEX.synchronize do
-        bar.done unless bar.max
         REMOVE << bar
+        Log::LAST.replace "remove"
       end
     end
 
@@ -220,7 +232,7 @@ module Log
       rescue KeepBar
         keep = true
       ensure
-        remove_bar(bar) unless bar
+        remove_bar(bar) if bar
       end
     end
   end

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

@@ -1,5 +1,5 @@
 module ConcurrentStream
-  attr_accessor :threads, :pids, :callback, :abort_callback, :filename, :joined, :autojoin
+  attr_accessor :threads, :pids, :callback, :abort_callback, :filename, :joined, :aborted, :autojoin
 
   def self.setup(stream, options = {}, &block)
     threads, pids, callback, filename, autojoin = Misc.process_options options, :threads, :pids, :callback, :filename, :autojoin
@@ -46,6 +46,10 @@ module ConcurrentStream
     @joined
   end
 
+  def aborted?
+    @aborted
+  end
+
   def join_threads
     if @threads and @threads.any?
       @threads.each do |t| 
@@ -97,11 +101,16 @@ module ConcurrentStream
   end
 
   def abort
-    abort_threads
-    abort_pids
-    @abort_callback.call if @abort_callback
-    @abort_callback = nil
-    @callback = nil
+    return if @aborted
+    begin
+      abort_threads
+      abort_pids
+      @abort_callback.call if @abort_callback
+    ensure
+      @abort_callback = nil
+      @callback = nil
+      @aborted = true
+    end
   end
 
   def super(*args)

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

@@ -47,8 +47,9 @@ module Misc
       lockfile.unlock if lockfile.locked?
       raise $!
     ensure
-      if unlock and lockfile.locked?
-        lockfile.unlock
+      if unlock 
+        lockfile.unlock if lockfile.locked?
+        FileUtils.rm lock_path if File.exists? lock_path
       end
     end
 

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

@@ -73,45 +73,6 @@ module Misc
     sout
   end
 
-  #def self.tee_stream_fork(stream)
-  #  stream_out1, stream_in1 = Misc.pipe
-  #  stream_out2, stream_in2 = Misc.pipe
-
-  #  splitter_pid = Process.fork do
-  #    Misc.purge_pipes(stream_in1, stream_in2)
-  #    stream_out1.close
-  #    stream_out2.close
-  #    begin
-  #      filename = stream.respond_to?(:filename)? stream.filename : nil
-  #      skip1 = skip2 = false
-  #      while block = stream.read(2048)
-  #        begin stream_in1.write block; rescue Exception;  Log.exception $!; skip1 = true end unless skip1 
-  #        begin stream_in2.write block; rescue Exception;  Log.exception $!; skip2 = true end unless skip2 
-  #      end
-  #      raise "Error writing in stream_in1" if skip1
-  #      raise "Error writing in stream_in2" if skip2
-  #      stream.join if stream.respond_to? :join
-  #      stream_in1.close 
-  #      stream_in2.close 
-  #    rescue Aborted
-  #      stream.abort if stream.respond_to? :abort
-  #      raise $!
-  #    rescue IOError
-  #      Log.exception $!
-  #    rescue Exception
-  #      Log.exception $!
-  #    end
-  #  end
-  #  stream.close
-  #  stream_in1.close
-  #  stream_in2.close
-
-  #  ConcurrentStream.setup stream_out1, :pids => [splitter_pid]
-  #  ConcurrentStream.setup stream_out2, :pids => [splitter_pid]
-
-  #  [stream_out1, stream_out2]
-  #end
-
   def self.tee_stream_thread(stream)
     stream_out1, stream_in1 = Misc.pipe
     stream_out2, stream_in2 = Misc.pipe
@@ -139,11 +100,14 @@ module Misc
         stream_in2.close unless stream_in2.closed?
         stream.join if stream.respond_to? :join
       rescue Aborted, Interrupt
-        Log.warn("Tee stream #{Misc.fingerprint stream} Aborted");
-        stream.abort if stream.respond_to? :abort
+        begin
+          stream.abort if stream.respond_to? :abort
+        rescue
+          Log.exception $!
+        end
       rescue Exception
         Log.exception $!
-        parent.raise $!
+        stream.abort if stream.respond_to? :abort
       end
     end
 
@@ -186,14 +150,17 @@ module Misc
     else
       begin
         while block = io.read(2048)
-          return if io.eof?
-          Thread.pass 
+          #return if io.eof?
+          #Thread.pass 
         end
         io.join if io.respond_to? :join
-      rescue IOError
-      rescue
-        Log.warn "Exception consuming stream: #{io.inspect}"
+      rescue Aborted
+        Log.warn "Consume stream aborted #{Misc.fingerprint io}"
         io.abort if io.respond_to? :abort
+      rescue Exception
+        Log.warn "Exception consuming stream: #{Misc.fingerprint io}: #{$!.message}"
+        io.abort if io.respond_to? :abort
+        raise $!
       end
     end
   end
@@ -244,11 +211,10 @@ module Misc
         rescue Aborted
           Log.warn "Aborted sensiblewrite -- #{ Log.reset << Log.color(:blue, path) }"
           content.abort if content.respond_to? :abort
-          content.join if content.respond_to? :join
+          Open.rm_f path if File.exists? path
         rescue Exception
           Log.warn "Exception in sensiblewrite: #{$!.message} -- #{ Log.color :blue, path }"
           content.abort if content.respond_to? :abort
-          content.join if content.respond_to? :join
           Open.rm_f path if File.exists? path
           raise $!
         ensure

data/lib/rbbt/workflow.rb

@@ -7,6 +7,8 @@ require 'rbbt/workflow/examples'
 
 module Workflow
 
+  STEP_CACHE = {}
+
   class TaskNotFoundException < Exception 
     def initialize(workflow, task = nil)
       if task
@@ -184,7 +186,7 @@ module Workflow
   end
 
   def step_cache
-    @step_cache ||= {}
+    @step_cache ||= Workflow::STEP_CACHE
   end
   
 
@@ -236,7 +238,7 @@ module Workflow
     step_path = step_path.call if Proc === step_path
     persist = input_values.nil? ? false : true
     key = Path === step_path ? step_path.find : step_path
-    step = Persist.memory("Step", :key => key, :repo => step_cache, :persist => persist ) do
+    step = Persist.memory("Step", :key => key, :repo => step_cache, :persist => persist) do
       step = Step.new step_path, task, input_values, dependencies
 
       helpers.each do |name, block|
@@ -244,8 +246,8 @@ module Workflow
           define_method name, &block
         end
       end
-      step
 
+      step
     end
 
     step.task ||= task

data/lib/rbbt/workflow/step.rb

@@ -71,23 +71,24 @@ class Step
     case 
     when IO === value
       begin
-        case @task.result_type
-        when :array
-          array = []
-          while line = value.gets
-            array << line.strip
-          end
-          array
-        when :tsv
-          TSV.open(value)
-        else
-          value.read
-        end
+        res = case @task.result_type
+              when :array
+                array = []
+                while line = value.gets
+                  array << line.strip
+                end
+                array
+              when :tsv
+                TSV.open(value)
+              else
+                value.read
+              end
+        value.join if value.respond_to? :join
+        res
       rescue Exception
         value.abort if value.respond_to? :abort
-      ensure
-        value.join if value.respond_to? :join
-        value.close unless value.closed?
+        self.abort
+        raise $!
       end
     when (not defined? Entity or description.nil? or not Entity.formats.include? description)
       value

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

@@ -1,6 +1,6 @@
 class Step
 
-  attr_reader :stream, :dupped
+  attr_reader :stream, :dupped, :saved_stream
 
   STREAM_CACHE = {}
   STREAM_CACHE_MUTEX = Mutex.new
@@ -67,7 +67,7 @@ class Step
     @mutex.synchronize do
       begin
         if IO === @result 
-          @result 
+          @saved_stream = @result 
         else 
           nil
         end
@@ -146,15 +146,23 @@ class Step
         unless dependency.result or dependency.done?
           dependency.run(true) 
         end
-      rescue Aborted, Interrupt
+      rescue Aborted
         backtrace = $!.backtrace
         set_info :backtrace, backtrace 
         log(:error, "Aborted dependency #{Log.color :yellow, dependency.task.name.to_s}")
+        self.abort
+        raise $!
+      rescue Interrupt
+        backtrace = $!.backtrace
+        set_info :backtrace, backtrace 
+        log(:error, "Interrupted dependency #{Log.color :yellow, dependency.task.name.to_s}")
+        self.abort
         raise $!
       rescue Exception
         backtrace = $!.backtrace
         set_info :backtrace, backtrace 
         log(:error, "Exception processing dependency #{Log.color :yellow, dependency.task.name.to_s} -- #{$!.class}: #{$!.message}")
+        self.abort
         raise $!
       end
     end
@@ -163,8 +171,8 @@ class Step
   def run(no_load = false)
     result = nil
 
-    begin
-      @mutex.synchronize do
+    @mutex.synchronize do
+      begin
         no_load = no_load ? :stream : false
         result = Persist.persist "Job", @task.result_type, :file => path, :check => checks, :no_load => no_load do |lockfile|
           if Step === Step.log_relay_step and not self == Step.log_relay_step
@@ -198,19 +206,18 @@ class Step
           begin
             result = _exec
           rescue Aborted
+            stop_dependencies
             log(:error, "Aborted")
-
-            kill_children
             raise $!
           rescue Exception
             backtrace = $!.backtrace
 
             # HACK: This fixes an strange behaviour in 1.9.3 where some
             # backtrace strings are coded in ASCII-8BIT
-            kill_children
             set_info :backtrace, backtrace 
             log(:error, "#{$!.class}: #{$!.message}")
             backtrace.each{|l| l.force_encoding("UTF-8")} if String.instance_methods.include? :force_encoding
+            stop_dependencies
             raise $!
           end
 
@@ -260,13 +267,9 @@ class Step
             end
             result.stream.abort_callback = Proc.new do
               begin
-                log :error, "#{Log.color :red, "ERROR -- streamming aborted"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}] -- #{path}"  if status == :streaming
                 stop_dependencies
-                abort_stream
-              rescue
-                Log.exception $!
-              ensure
-                join
+                log :error, "#{Log.color :red, "ERROR -- streamming aborted"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}] -- #{path}"  if status == :streaming
+              rescue Exception
               end
             end
           else
@@ -284,9 +287,9 @@ class Step
         else
           @result = prepare_result result, @task.result_description
         end
+      rescue Exception
+        self.abort
       end
-    ensure
-      join unless no_load
     end
   end
 
@@ -300,7 +303,7 @@ class Step
           res = run true
         rescue Aborted
           Log.debug{"Forked process aborted: #{path}"}
-          log :aborted, "Aborted"
+          log :aborted, "Job aborted (#{Process.pid})"
           raise $!
         rescue Exception
           Log.debug("Exception '#{$!.message}' caught on forked process: #{path}")
@@ -340,11 +343,15 @@ class Step
 
   def stop_dependencies
     dependencies.each do |dep|
+      Log.warn "Stoping #{Misc.fingerprint dep}"
       begin
-        dep.abort unless dep.done? or dep.error? or dep.aborted?
+        dep.abort unless dep.done?
+      rescue Exception
+        Log.exception $!
       rescue Aborted
       end
     end
+    kill_children
   end
 
   def abort_pid
@@ -371,27 +378,42 @@ class Step
 
   def abort_stream
     stream = get_stream if @result
-    stream ||= @stream 
-    if stream and stream.respond_to? :abort
-      Log.medium "Aborting stream #{stream.inspect} -- #{Log.color :blue, path}"
+    stream ||= @saved_stream 
+    if stream and stream.respond_to? :abort and not stream.aborted?
       begin
+        Log.medium "Aborting job stream #{stream.inspect} -- #{Log.color :blue, path}"
         stream.abort 
+        Log.medium "Aborted job stream #{stream.inspect} -- #{Log.color :blue, path}"
+        #stream.close unless stream.closed?
       rescue Aborted
+        Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}"
+        retry
       end
     end
   end
 
   def abort
+    return if @aborted
     Log.medium{"#{Log.color :red, "Aborting"} #{Log.color :blue, path}"}
     begin
-      abort_pid
       stop_dependencies
+      @aborted = true
       abort_stream
-    rescue
+      abort_pid
+    rescue Aborted
+      Log.medium{"#{Log.color :red, "Aborting ABORTED RETRY"} #{Log.color :blue, path}"}
+      retry
+    rescue Exception
       Log.exception $!
     ensure
-      log(:aborted, "Job aborted")
+      @aborted = true
+      begin
+        log(:aborted, "Job aborted")
+      rescue Exception
+        Log.exception $!
+      end
     end
+    Log.medium{"#{Log.color :red, "Aborted"} #{Log.color :blue, path}"}
   end
 
   def join_stream
@@ -401,9 +423,9 @@ class Step
         Misc.consume_stream stream
         stream.join if stream.respond_to? :join 
       rescue Exception
-        stream.abort if stream.respond_to? :abort 
         self.abort
         raise $!
+        #stream.abort if stream.respond_to? :abort 
       end
     end
   end

data/share/rbbt_commands/workflow/example

@@ -13,27 +13,33 @@ def run_task(workflow, task, name)
   ARGV.replace([workflow.to_s, task, '--load_inputs', example_dir, '--jobname', name,'-pf'] + $saved_args)
 
   path = nil
+  success = nil
   TmpFile.with_file do |res|
     Open.open(res, :mode => 'w') do |file|
       @pid = Process.fork{
         STDOUT.reopen res
         load Rbbt.share.rbbt_commands.workflow.task.find
       }
-      file.close
       Signal.trap(:INT) do
         begin
           Process.kill "INT", @pid
         ensure
-          exit -1
+          Kernel.exit! -1
         end
       end
-      Process.wait @pid
+      file.close
+      begin
+        p,s = Process.waitpid2 @pid
+        success = s.success?
+      rescue Errno::ECHILD
+        success = true
+      end
     end
     path = Open.read(res).strip if File.exists? res
   end
   path = "NO RESULT" if path.nil? or path.empty?
 
-  if $?.success?
+  if success
     Log.info "#{Log.color :green, "SUCCESS"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
     return [path, true]
   else
@@ -60,14 +66,15 @@ workflow = Workflow.require_workflow workflow
 tasks = task ? [task] : workflow.libdir.examples.glob('*').collect{|file| File.basename file }
 
 task_result = {}
-tasks.each do |task|
+TSV.traverse tasks, :threads => 5 do |task|
   names = name ? [name] : workflow.libdir.examples[task].glob('*').collect{|file| File.basename file }
-  names.each do |name|
+  TSV.traverse names, :threads => 5 do |name|
     success = run_task workflow, task, name
     task_result[[task, name]] = success
   end
 end
 
+
 task_result.each do |code,res|
   task, name = code
   path, success = res

data/share/rbbt_commands/workflow/task

@@ -309,14 +309,6 @@ begin
       exit 0
     end
 
-    Signal.trap(:INT) do
-      begin
-        job.abort if job.info[:pid] == job.pid
-      rescue
-      end
-      exit 0
-    end
-
     job.fork
   else
     job.run(true)
@@ -407,6 +399,7 @@ if options.delete(:list_job_files)
 end
 
 if job_file = options.delete(:job_file)
+  job.join
   file = job.file(job_file)
   out.puts Path === file ? file.read : file
   exit 0

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

@@ -2,6 +2,8 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/tsv'
 require 'rbbt/tsv/parallel'
 
+class StopException < StandardError; end
+
 class TestTSVParallelThrough < Test::Unit::TestCase
 
   def _test_traverse_tsv
@@ -307,16 +309,16 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
     cpus = 2
 
-
-    3.times do
+    20.times do
+      Log.info Log.color :red, "TRAVERSE EXCEPTION"
       stream = Organism.identifiers("Hsa/jun2011").open 
       dumper = TSV::Dumper.new Organism.identifiers("Hsa/jun2011").tsv_options
       dumper.init
 
-      assert_raise do
+      assert_raise StopException do
         TSV.traverse stream, :head => head,  :cpus => cpus, :into => dumper do |k,v|
           k = k.first
-          raise "STOP" if rand(100) < 1
+          raise StopException if rand(100) < 1
           [k,v]
         end
         stream = dumper.stream

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

@@ -35,7 +35,7 @@ class TestProgress < Test::Unit::TestCase
           bar.tick
           sleep 0.3
         end
-        Log.debug "Done progress"
+        #Log.debug "Done progress"
         assert bar.history.length > 0
       end
     end
@@ -46,7 +46,7 @@ class TestProgress < Test::Unit::TestCase
           bar.tick
           sleep 0.2
         end
-        Log.debug "Done progress"
+        #Log.debug "Done progress"
         assert bar.history.length > 0
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.2
+  version: 5.13.3
 platform: ruby
 authors:
 - Miguel Vazquez