rbbt-util 5.13.20 → 5.13.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 66e0264c3104ab53b278845aaab51e2ae75b5d40
-  data.tar.gz: 7abc522ee044b2527b0a6a40acff4a8fde3c7c90
+  metadata.gz: abdf8f28beb9196592b55ba4bce0a36931c8f880
+  data.tar.gz: eaacc6b9157a3edafe34c6b3b2db9435c9d9dd08
 SHA512:
-  metadata.gz: 925b812e86aed64d95cb08b6f56491518640953f8284168bbefd21e5500989b9a6a8755df667d552115f908a5e4913b4d9c5fac3b9fba2214c66e0162c492c1e
-  data.tar.gz: 0af9ab272db85087c7c2244d894a0af2c68867c93117d6d1e594bb676b59978bdb1fa5790e915204be8a2423187713b344b02d56af19abcd9ac19d146bc61b6c
+  metadata.gz: c832c458e7434da05bdd203097e787815e35b444c12faf1d6e6de423b2d282528c2a9ed4c379be8580c65b6d71fa01d8595ebf313e59de0dddc1ef3ba2e4ce5a
+  data.tar.gz: f37553cde0d158988bde704bb73f014d4e8e2d311447d37f87ee61bae7bd314d8e54263438dfce9d22aabf3258b862b87d3fbf910ec4d2f61eb066e75f41d30d

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

@@ -29,11 +29,12 @@ class RbbtProcessQueue
           end
         rescue Aborted
           Log.warn "Callback thread aborted"
-          @process_monitor.raise Aborted.new
+          @process_monitor.raise $!
           raise $!
         rescue ClosedStream
         rescue Exception
           Log.warn "Callback thread exception: #{$!.message}"
+          Log.exception $!
           @process_monitor.raise $!
           raise $!
         ensure

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

@@ -1,4 +1,6 @@
-Lockfile.refresh = false #if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
+Lockfile.refresh = 5 * 60 #if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
+Lockfile.max_age = 60 * 60 * 5
+Lockfile.refresh=false
 
 module Misc
 

data/lib/rbbt/workflow/accessor.rb

@@ -5,6 +5,18 @@ class Step
    
   INFO_SERIALIAZER = Marshal
 
+  def self.wait_for_jobs(jobs)
+    begin
+      threads = []
+      jobs.each do |j| threads << Thread.new{j.grace.join} end
+      threads.each{|t| t.join }
+    rescue Exception
+      threads.each{|t| t.exit }
+      jobs.each do |j| j.abort end
+      raise $!
+    end
+  end
+
   def self.files_dir(path)
     path.nil? ? nil : path + '.files'
   end

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

@@ -246,8 +246,6 @@ class Step
                 log :aborted, "#{Log.color :red, "Aborted"} #{Log.color :yellow, task.name.to_s || ""}" if status == :streaming
               rescue
                 Log.exception $!
-              ensure
-                join
               end
             end
           else

data/share/rbbt_commands/workflow/info

@@ -0,0 +1,81 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/workflow'
+
+require 'rbbt-util'
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Examine the info of a job result
+
+$ rbbt workflow info <job-result>
+
+-h--help Help
+EOF
+
+SOPT.usage if options[:help]
+
+file = ARGV.shift
+
+def get_step(file)
+  file = file.sub(/\.(info|files)/,'')
+  Step.new file
+end
+
+def status_msg(status)
+  color = case status
+          when :error, :aborted, :missing
+            :red
+          when :streaming
+            :yellow
+          when :done
+            :green
+          else
+            nil
+          end
+  Log.color(color, status)
+end
+
+step = get_step file
+
+info = step.info
+dependencies = info[:dependencies]
+inputs = info[:inputs]
+status = info[:status]
+time = info[:time_elapsed]
+messages = info[:messages]
+
+puts Log.color(:magenta, "File") << ": " << step.path
+puts Log.color(:magenta, "Status") << ": " << status_msg(status)
+puts Log.color(:magenta, "Time") << ": " << time.to_i.to_s << " sec." if time
+if inputs and inputs.any?
+  puts Log.color(:magenta, "Inputs")
+  inputs.each do |input,value|
+    case value
+    when Array
+      puts "  " << Misc.format_definition_list_item(input, value[0..5]*"\n", 80, 20, :blue)
+    when TrueClass, FalseClass
+      puts "  " << Misc.format_definition_list_item(input, value.to_s, 80, 20, :blue)
+    else
+      text = value.split("\n")[0..5].compact * "\n\n"
+      puts "  " << Misc.format_definition_list_item(input, text, 80, 20, :blue)
+    end
+  end
+end
+
+if dependencies and dependencies.any?
+  puts Log.color(:magenta, "Dependencies") << ": "
+  dependencies.each do |name,task,file|
+    puts "  " << file
+  end 
+end
+
+if messages and messages.any?
+  puts Log.color(:magenta, "Messages") << ": "
+  messages.each do |msg|
+    puts "  " << msg
+  end 
+end

data/share/rbbt_commands/workflow/prov

@@ -8,6 +8,21 @@ require 'rbbt/util/simpleopt'
 require 'rbbt/workflow/step'
 require 'rbbt/util/misc'
 
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Examine the provenance of a job result
+
+$ rbbt workflow prov <job-result>
+
+-h--help Help
+EOF
+
+SOPT.usage if options[:help]
+
 file = ARGV.shift
 
 $seen = []

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.20
+  version: 5.13.21
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-26 00:00:00.000000000 Z
+date: 2014-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -258,6 +258,7 @@ files:
 - share/rbbt_commands/tsv/values
 - share/rbbt_commands/workflow/cmd
 - share/rbbt_commands/workflow/example
+- share/rbbt_commands/workflow/info
 - share/rbbt_commands/workflow/install
 - share/rbbt_commands/workflow/jobs
 - share/rbbt_commands/workflow/list