rbbt-util 5.9.5 → 5.9.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: f8f7fee0f9f2ceccc294431d31d1f9e14983b903
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+  data.tar.gz: a3c428d4dc3898f04842ce9f71bc272a1650525c
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data/bin/rbbt

@@ -2,9 +2,6 @@
 
 require 'rbbt'
 require 'rbbt/util/simpleopt'
-require 'highline'
-
-Log.tty_size = HighLine::SystemExtensions.terminal_size.first
 
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit

data/lib/rbbt/util/log.rb

@@ -16,6 +16,8 @@ module Log
     attr_accessor :logfile, :severity, :nocolor, :tty_size
   end
   self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
+  require 'highline'
+  self.tty_size = HighLine::SystemExtensions.terminal_size.first
 
 
   def self.with_severity(level)
@@ -54,7 +56,11 @@ module Log
   end
 
   def self.return_line
-    "\033[1A"
+    nocolor ? "" : "\033[1A"
+  end
+
+  def self.clear_line(out = STDOUT)
+    out.puts Log.return_line << " " * Log.tty_size << Log.return_line unless nocolor
   end
 
   def self.highlight(str = nil)

data/lib/rbbt/util/misc.rb

@@ -16,8 +16,8 @@ class Hash
   end
 end
 
-class ParameterException < StandardError; end
-class FieldNotFoundError < StandardError;end
+class ParameterException < Exception; end
+class FieldNotFoundError < Exception;end
 class Aborted < Exception; end
 class TryAgain < Exception; end
 class ClosedStream < Exception; end
@@ -173,34 +173,6 @@ module Misc
     [colors, used]
   end
 
-  #def self.collapse_ranges_old(ranges)
-  #  processed = []
-  #  last = nil
-  #  ranges.sort_by{|range| range.begin }.each do |range|
-  #    rbegin = range.begin
-  #    rend = range.end
-  #    if last.nil? or rbegin > last
-  #      processed << range
-  #      last = rend
-  #    else
-  #     new_processed = []
-  #      processed.each do |processed_range|
-  #        if processed_range.end < rbegin
-  #          new_processed << processed_range
-  #        else
-  #          eend = [rend, processed_range.end].max
-  #          new_processed << (processed_range.begin..eend)
-  #          break
-  #        end
-  #      end
-  #      processed = new_processed
-  #      last = rend if rend > last
-  #    end
-  #  end
-  #
-  #  processed
-  #end
-
   def self.collapse_ranges(ranges)
     processed = []
     last = nil

data/lib/rbbt/workflow/step.rb

@@ -232,8 +232,6 @@ class Step
     else
       Log.medium "Aborting #{path}: #{ @pid }"
       begin
-        Process.kill("TERM", @pid)
-        sleep 1
         Process.kill("KILL", @pid)
         Process.waitpid @pid
       rescue Exception
@@ -284,9 +282,9 @@ class Step
     # placed. In that case, do not consider its dependencies
     return [] if self.done? and not Open.exists? self.info_file
 
-    @dependencies.collect{|step| 
+    dependencies.collect{|step| 
       step.rec_dependencies 
-    }.flatten.concat  @dependencies
+    }.flatten.concat  dependencies
   end
 
   def recursive_clean

data/share/rbbt_commands/workflow/task

@@ -250,7 +250,7 @@ begin
     exit 0
   end
 
-  if do_exec
+  if do_exec or (job.respond_to?(:is_exec) and job.is_exec)
     res = job.exec
     case
     when Array === res
@@ -283,36 +283,6 @@ begin
 
     job.fork
 
-    puts 
-    puts
-    size = Log.tty_size
-    size = 100 if size.nil?
-
-    while not job.done?
-      message = (job.messages and job.messages.any?) ? job.messages.last.strip : "no message"
-      status = job.status || "no status"
-      if job.info and job.info.include? :issued
-        issued = job.info[:issued]
-        issued = Time.parse(issued) unless Time === issued
-        time = Time.now - issued
-      end
-      puts Log.return_line << " " * size << Log.return_line 
-      puts Log.return_line << " " * size << Log.return_line 
-      puts "#{Log.color :blue, job.path}"
-      puts "Waiting on #{Log.color :blue, job.info[:pid] || job.pid} (#{time ? time.to_i : '?'} sec. ago) " << [Log.color(:cyan, status.to_s),message.strip].compact*" " 
-      sleep 2
-    end
-    raise job.messages.last if job.error?
-
-    if job.info and job.info.include? :issued
-      issued = job.info[:issued]
-      issued = Time.parse(issued) unless Time === issued
-      time = Time.now - issued
-    end
-    puts Log.return_line << " " * size << Log.return_line 
-    puts Log.return_line << " " * size << Log.return_line 
-    puts job.path
-    exit 0
   else
     job.run(true)
     res = job
@@ -337,6 +307,47 @@ begin
   else
     Log.low "Job name: #{job.name}" 
   end
+
+  if do_fork
+    puts
+    space = 1
+    Log.tty_size ||= 100
+
+    while not job.done?
+      message = (job.messages and job.messages.any?) ? job.messages.last.strip : "no message"
+      status = job.status || "no status"
+      if job.info and job.info.include? :issued
+        issued = job.info[:issued]
+        issued = Time.parse(issued) unless Time === issued
+        time = Time.now - issued
+      end
+
+
+      space.times do
+        Log.clear_line 
+      end
+
+      puts "#{Log.color :blue, job.path}"
+      str = "Waiting on #{Log.color :blue, job.info[:pid] || job.pid} (#{time ? time.to_i : '?'} sec. ago) " << [Log.color(:cyan, status.to_s),message.strip].compact*" "
+      puts Misc.format_paragraph str, Log.tty_size
+
+      space = 2 + Log.uncolor(str).length / Log.tty_size
+      sleep 2
+    end
+    raise job.messages.last if job.error?
+
+    if job.info and job.info.include? :issued
+      issued = job.info[:issued]
+      issued = Time.parse(issued) unless Time === issued
+      time = Time.now - issued
+    end
+
+    space.times do
+      Log.clear_line 
+    end
+    out.puts job.path
+    exit 0
+  end
 rescue ParameterException
   SOPT.delete_inputs(workflow.rec_inputs(task.name))
   usage(workflow, task, $!)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.5
+  version: 5.9.6
 platform: ruby
 authors:
 - Miguel Vazquez