rbbt-util 5.6.8 → 5.6.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 7ceb01cd346987e440d5ded8aec7e741ade11831
+  metadata.gz: 3a45eff8cafc9d26b4eb4e6c670af1d2fe17ec0d
+  data.tar.gz: e889c0fafcc84778750f7093ed9a1a408de7c31f
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-  data.tar.gz: 87d12e3c415a8bf309b952dbc71ab73d40912e19d3e28a123fc2e5aedac661759129c62529e2cdc6fe5c5a47044e4549ccfa1daa6a7cc00986a6d304ca517ff6
+  metadata.gz: f7dccdd9729516b74d7ab8ab162d7290e5b4e4485efc1839bea45bba479b088641b988320f994fd0e4ee0d27a29fa1f671a7a7fd171261ab9ceaea50479a5bf6
+  data.tar.gz: 5e1531954628ba52e9afd7f57690af8f3955c7bbab949235ca2c537a71270677ac19eaf64d16d8f168f7322b5c09b29c0dfdd7aac0fb857ad4774d3e99d31c98

data/bin/rbbt

@@ -3,9 +3,9 @@
 require 'rbbt'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):-cd--command_dir* Directory from where to load commands:--profile Profile execution:--no_color Disable colored output:--locate_file Locate file been executed")
+options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):-cd--command_dir* Directory from where to load commands:--profile Profile execution:--nocolor Disable colored output:--locate_file Locate file been executed")
 
-ENV["RBBT_NOCOLOR"] = "true" if options[:no_color]
+Log.nocolor = true if options[:nocolor]
 locate = options.delete :locate_file
 
 if options[:log]
@@ -67,12 +67,12 @@ def rbbt_usage(prev = nil)
 end
 
 def print_error(error, backtrace = nil)
-  puts Term::ANSIColor.red("Error:")
+  puts Log.color :red, "Error:"
   puts
   puts error
   if backtrace
     puts
-    puts Term::ANSIColor.red("Backtrace:")
+    puts Log.color :red, "Backtrace:"
     puts
     puts backtrace * "\n"
   end
@@ -109,6 +109,7 @@ begin
   exit 0
 
 rescue ParameterException
+  ddd "EXCEPTION"
   puts
   rbbt_usage
   print_error($!.message, $!.backtrace)

data/etc/app.d/init.rb

@@ -7,5 +7,3 @@ require 'rbbt/rest/entity'
 require 'rbbt/rest/workflow'
 require 'rbbt/rest/file_server'
 require 'rbbt/rest/helpers'
-
-YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler

data/lib/rbbt/util/log.rb

@@ -13,8 +13,9 @@ module Log
   ERROR    = 6
 
   class << self
-    attr_accessor :logfile, :severity
+    attr_accessor :logfile, :severity, :nocolor
   end
+  self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
 
 
   def self.logfile
@@ -23,16 +24,11 @@ module Log
 
   WHITE, DARK, GREEN, YELLOW, RED = Color::SOLARIZED.values_at :base0, :base00, :green, :yellow, :magenta
 
-  if ENV["RBBT_NOCOLOR"] == "true"
-    SEVERITY_COLOR = [reset, "", "", "", "", "", ""] #.collect{|e| "\033[#{e}"}
-  else
-    SEVERITY_COLOR = [reset, cyan, green, magenta, blue, yellow, red] #.collect{|e| "\033[#{e}"}
-  end
-
+  SEVERITY_COLOR = [reset, cyan, green, magenta, blue, yellow, red] #.collect{|e| "\033[#{e}"}
   HIGHLIGHT = "\033[1m"
 
   def self.color(severity, str = nil)
-    return str || "" if ENV["RBBT_NOCOLOR"] == "true"
+    return str || "" if nocolor 
     color = SEVERITY_COLOR[severity] if Fixnum === severity
     color = Term::ANSIColor.send(severity) if Symbol === severity and Term::ANSIColor.respond_to? severity 
     if str.nil?
@@ -44,8 +40,10 @@ module Log
 
   def self.highlight(str = nil)
     if str.nil?
+      return "" if nocolor
       HIGHLIGHT
     else
+      return str if nocolor
       HIGHLIGHT + str + color(0)
     end
   end
@@ -118,7 +116,7 @@ end
 
 def ppp(message)
   stack = caller
-  puts "#{Log::SEVERITY_COLOR[1]}PRINT:#{Log::SEVERITY_COLOR[0]} " << stack.first
+  puts "#{Log.color :cyan, "PRINT:"} " << stack.first
   puts ""
   puts "=> " << message
   puts ""
@@ -126,7 +124,7 @@ end
 
 def ddd(message, file = $stdout)
   stack = caller
-  Log.debug{"#{Log::SEVERITY_COLOR[1]}DEVEL:#{Log::SEVERITY_COLOR[0]} " << stack.first}
+  Log.debug{"#{Log.color :cyan, "DEBUG:"} " << stack.first}
   Log.debug{""}
   Log.debug{"=> " << message.inspect}
   Log.debug{""}
@@ -134,7 +132,7 @@ end
 
 def fff(object)
   stack = caller
-  Log.debug{"#{Log::SEVERITY_COLOR[1]}FINGERPRINT:#{Log::SEVERITY_COLOR[0]} " << stack.first}
+  Log.debug{"#{Log.color :cyan, "FINGERPRINT:"} " << stack.first}
   Log.debug{""}
   Log.debug{require 'rbbt/util/misc'; "=> " << Misc.fingerprint(object) }
   Log.debug{""}

data/lib/rbbt/util/misc.rb

@@ -932,7 +932,7 @@ end
 
     begin
       if File.exists? lockfile and
-        Misc.hostname == (info = YAML.load_file(lockfile))["host"] and 
+        Misc.hostname == (info = Open.open(lockfile){|f| YAML.load(f) })["host"] and 
         info["pid"] and not Misc.pid_exists?(info["pid"])
 
         Log.info("Removing lockfile: #{lockfile}. This pid #{Process.pid}. Content: #{info.inspect}")
@@ -945,11 +945,12 @@ end
 
     begin
       lockfile.lock do 
-        res = yield file, *args
+        yield file, *args
       end
     rescue Interrupt
       Log.error "Process #{Process.pid} interrupted while in lock: #{ lock_path }"
       raise $!
+    ensure
     end
 
     res
@@ -1362,8 +1363,8 @@ end
 
 
   def self.zip_fields(array)
-    return [] if array.empty?
-    array[0].zip(*array[1..-1])
+    return [] if array.empty? or (first = array.first).nil?
+    first.zip(*array[1..-1])
   end
 
   def self.camel_case(string)

data/lib/rbbt/util/open.rb

@@ -330,9 +330,7 @@ module Open
            # What about grep?
            wget(url, wget_options)
          when (options[:nocache] != :update and in_cache(url, wget_options))
-           Misc.lock(in_cache(url, wget_options)) do
-             file_open(in_cache(url, wget_options), options[:grep], mode, options[:invert_grep])
-           end
+           file_open(in_cache(url, wget_options), options[:grep], mode, options[:invert_grep])
          else
            io = wget(url, wget_options)
            add_cache(url, io, wget_options)

data/share/rbbt_commands/workflow/monitor

@@ -8,8 +8,6 @@ require 'rbbt/util/misc'
 
 options = SOPT.get("-l--list:-z--zombies:-e--errors:-c--clean:-n--name:-a--all:-w--wipe:-f--file*:-q--quick:-d--directory*")
 
-YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
-
 def info_files
   Dir.glob('**/*.info')
 end

data/share/rbbt_commands/workflow/provenance

@@ -12,9 +12,6 @@ require 'rbbt/util/misc'
 
 $workdir = Path.setup(File.expand_path(ARGV[0] || '.'))
 
-
-YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
-
 def info_files
   $workdir.glob(Step.info_file('**/*'))
 end

data/share/rbbt_commands/workflow/task

@@ -4,8 +4,6 @@ require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
 require 'rbbt/workflow/usage'
 
-YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
-
 def load_inputs(dir, task)
   inputs = {}
   dir = Path.setup(dir.dup)
@@ -43,8 +41,8 @@ def usage(workflow = nil, task = nil, exception=nil)
     workflow.doc(task)
   end
 
-  raise exception if exception
-  exit 0
+  print_error(exception.message, exception.backtrace) if exception
+  exit -1
 end
 
 def SOPT_options(workflow, task)

data/test/rbbt/util/test_misc.rb

@@ -1,3 +1,5 @@
+#ENV['LOCKFILE_DEBUG'] = "true";; require 'lockfile'
+
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/util/misc'
 require 'test/unit'
@@ -283,4 +285,14 @@ class TestMisc < Test::Unit::TestCase
     assert time_spent <= (t+1) * 0.5
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }"}, lines
   end
+
+  def __test_lock_fd
+    require 'rbbt/workflow'
+    Rbbt.var.jobs.Structure.neighbour_map.glob("*")[0..1000].each do |file|
+      next if file =~ /\.info$/
+      step = Step.new file
+      TSV.open step.path
+    end
+    puts `ls -l /proc/#{ Process.pid }/fd`
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.8
+  version: 5.6.9
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-24 00:00:00.000000000 Z
+date: 2014-02-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake