rbbt-util 5.13.24 → 5.13.25

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 47850a9f40b69fc8cb761dbefea3aec895c1c955
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+  data.tar.gz: eef931195c348851b6aeb3de3ba35f4e043884f6
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+  data.tar.gz: 50a0e08c13bb120b2b111de91f6446eb9d42cd0b6ca1897e8a2308e1f547cf2bb7d4d1198eeecf89ce2c2bf457456e3234403726cbdc314c2dcd8519187ee33f

data/bin/rbbt

@@ -1,8 +1,34 @@
 #!/usr/bin/env ruby
 
+dev_dir = nil
+if _i = ARGV.index("--dev")
+  dev_dir = ARGV[_i+1]
+  ARGV.delete "--dev"
+end
+
+if dev_dir.nil? 
+  _s = nil
+  ARGV.each_with_index do |s,i|
+    if s.match(/^--dev(?:=(.*))?/)
+      dev_dir = $1
+      _s = s
+      next
+    end
+  end
+  ARGV.delete _s if _s
+end
+
+if dev_dir
+  Dir.glob(File.join(File.expand_path(dev_dir),'rbbt-*')).each do |f|
+    $LOAD_PATH << f
+  end
+end
+
 require 'rbbt'
 require 'rbbt/util/simpleopt'
 
+Log.nocolor = true if ARGV.include? "--nocolor"
+
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit
 
@@ -10,6 +36,7 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
 
 
 --log*                  #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}
+--dev*                  #{Log.color :yellow, "Find development libraries in the directory specified"}
 -cd--command_dir*       #{Log.color :yellow, "Directory from where to load command scripts"}
 --profile               #{Log.color :yellow, "Profile execution"}
 --nocolor               #{Log.color :yellow, "Disable colored output"}
@@ -17,10 +44,6 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
 --locate_file           #{Log.color :yellow, "Report the location of the script instead of executing it"}
 EOF
 
-if options[:nocolor]
-  Log.nocolor = true 
-end
-
 if options.delete :nobar
   ENV["RBBT_NO_PROGRESS"] = "true"
 end
@@ -29,7 +52,14 @@ locate = options.delete :locate_file
 
 if options[:log]
   Log.severity = options[:log].to_i
-  SOPT.input_descriptions.each{|t,d| d.replace Log.uncolor(d) }
+else
+  global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
+  if ENV["RBBT_LOG"]
+    Log.severity = ENV["RBBT_LOG"].to_i 
+  else
+    global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
+    Log.severity = global_severity.to_i if global_severity
+  end
 end
 
 if options[:command_dir]

data/lib/rbbt/resource.rb

@@ -65,7 +65,8 @@ module Resource
     begin
       @server_missing_resource_cache ||= Set.new
       raise "Resource Not Found" if @server_missing_resource_cache.include? url
-      Net::HTTP.get_response URI(url) do |response|
+      Misc.lock final_path do
+        Net::HTTP.get_response URI(url) do |response|
           case response
           when Net::HTTPSuccess, Net::HTTPOK
             Misc.sensiblewrite(final_path) do |file|
@@ -77,15 +78,19 @@ module Resource
             location = response['location']
             Log.debug("Feching directory from: #{location}. Into: #{final_path}")
             FileUtils.mkdir_p final_path unless File.exists? final_path
-            Misc.in_dir final_path do
-              CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+            TmpFile.with_file do |tmp_dir|
+              Misc.in_dir tmp_dir do
+                CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+              end
             end
+            File.utils tmp_dir, final_path
           when Net::HTTPInternalServerError
             @server_missing_resource_cache << url
             raise "Resource Not Found"
           else
             raise "Response not understood: #{response.inspect}"
           end
+        end
       end
     rescue
       Log.warn "Could not retrieve (#{self.to_s}) #{ path } from #{ remote_server }"

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

@@ -459,6 +459,7 @@ module TSV
         stream.abort if stream and stream.respond_to? :abort
         stream = obj_stream(into)
         stream.abort if stream and stream.respond_to? :abort
+        parent.raise $!
         raise $!
       end
     end

data/lib/rbbt/util/log.rb

@@ -205,7 +205,7 @@ module Log
     error("BACKTRACE:\n" + e.backtrace * "\n") 
   end
 
-  case ENV['RBBT_LOG']
+  case ENV['RBBT_LOG'] 
   when 'DEBUG' 
     self.severity = DEBUG
   when 'LOW' 

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

@@ -54,10 +54,6 @@ module ConcurrentStream
     if @threads and @threads.any?
       @threads.each do |t| 
         t.join unless t == Thread.current
-        #begin
-        #ensure
-        #  t.join unless t == Thread.current
-        #end
       end
       @threads = []
     end
@@ -94,7 +90,33 @@ module ConcurrentStream
   end
 
   def abort_threads
-    @threads.each{|t| t.raise Aborted.new unless t == Thread.current } if @threads
+    Log.medium "Aborting threads (#{Thread.current.inspect}) #{@threads.collect{|t| t.inspect } * ", "}"
+
+    @threads.each do |t| 
+      @aborted = false if t == Thread.current
+      next if t == Thread.current
+      Log.medium "Aborting thread #{t.inspect}"
+      t.raise Aborted.new "Hey"
+    end if @threads
+
+    sleeped = false
+    @threads.each do |t|
+      next if t == Thread.current
+      if t.alive? 
+        sleep 1 unless sleeped
+        sleeped = true
+        Log.medium "Kill thread #{t.inspect}"
+        t.kill
+      end
+      begin
+        Log.medium "Join thread #{t.inspect}"
+        t.join unless t == Thread.current
+      rescue Aborted
+      rescue Exception
+        Log.exception $!
+      end
+    end
+    Log.medium "Aborted threads (#{Thread.current.inspect}) #{@threads.collect{|t| t.inspect } * ", "}"
   end
 
   def abort_pids
@@ -103,9 +125,9 @@ module ConcurrentStream
   end
 
   def abort
-    Log.medium "Aborting stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
     return if @aborted
-    @aborted = true
+    Log.medium "Aborting stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
+    @aborted = true 
     begin
       @callback = nil
       @abort_callback.call if @abort_callback
@@ -115,6 +137,7 @@ module ConcurrentStream
       abort_threads
       abort_pids
     end
+    Log.medium "Aborted stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
   end
 
   def super(*args)

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

@@ -358,6 +358,7 @@ class Step
         #stream.close unless stream.closed?
       rescue Aborted
         Log.medium "Aborting job stream #{stream.inspect} ABORTED RETRY -- #{Log.color :blue, path}"
+        Log.exception $!
         retry
       end
     end

data/share/rbbt_commands/log

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Change log level
+
+$ rbbt log <level>
+
+DEBUG
+LOW
+MEDIUM
+HIGH
+INFO
+WARN
+ERROR
+
+-h--help Print this help
+
+EOF
+rbbt_usage and exit 0 if options[:help] 
+if ARGV.empty?
+  puts Rbbt.etc.log_severity.read
+else
+  Open.write(Rbbt.etc.log_severity, ARGV[0].upcase)
+end
+
+

data/share/rbbt_commands/workflow/info

@@ -55,6 +55,8 @@ if inputs and inputs.any?
   puts Log.color(:magenta, "Inputs")
   inputs.each do |input,value|
     case value
+    when nil
+      puts "  " << Misc.format_definition_list_item(input, 'nil', 80, 20, :blue)
     when Array
       puts "  " << Misc.format_definition_list_item(input, value[0..5]*"\n", 80, 20, :blue)
     when TrueClass, FalseClass

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.24
+  version: 5.13.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-29 00:00:00.000000000 Z
+date: 2014-05-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -236,6 +236,7 @@ files:
 - share/rbbt_commands/file_server/add
 - share/rbbt_commands/file_server/list
 - share/rbbt_commands/file_server/remove
+- share/rbbt_commands/log
 - share/rbbt_commands/resource/exists
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get