rbbt-util 5.13.21 → 5.13.22

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: eaacc6b9157a3edafe34c6b3b2db9435c9d9dd08
+  metadata.gz: 3a19d56208ed15434da77c5823b332526972ac70
+  data.tar.gz: 0d1296b74615471612be8717e6530c1cdf687147
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+  data.tar.gz: 5da483b8a7179b5fd9e9f9b49c1eed1024a7d3d78af15df4cc28f6af66472f8572e4de0840ca2b2bbca24f624abf1d8002e019330d42b304cea03f4cf1543481

data/lib/rbbt/workflow.rb

@@ -239,7 +239,7 @@ module Workflow
     persist = false
     key = Path === step_path ? step_path.find : step_path
     step = Persist.memory("Step", :key => key, :repo => step_cache, :persist => persist) do
-      step = Step.new step_path, task, input_values, dependencies
+    step = Step.new step_path, task, input_values, dependencies
 
       helpers.each do |name, block|
         (class << step; self; end).instance_eval do
@@ -270,7 +270,15 @@ module Workflow
 
     dependencies = real_dependencies(task, jobname, inputs, task_dependencies[taskname] || [])
 
-    if inputs.empty?
+    real_inputs = {}
+    task_inputs = task_info(taskname)[:inputs]
+    defaults = task_info(taskname)[:input_defaults]
+
+    inputs.each do |k,v|
+      real_inputs[k] = v if task_inputs.include?(k) and defaults[k].to_s != v.to_s and not (FalseClass === v and defaults[k].nil?)
+    end
+
+    if real_inputs.empty?
       step_path = step_path taskname, jobname, [], [], task.extension
       input_values = task.take_input_values(inputs)
     else

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

@@ -445,8 +445,8 @@ class Step
         pid = nil
         dependencies.each{|dep| dep.join }
       end
-      self
       sleep 1 until path.exists?
+      self
     ensure
       set_info :joined, true
     end

data/share/rbbt_commands/workflow/server

@@ -18,12 +18,12 @@ workflow = ARGV.first
 
 YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
 
-Workflow.require_workflow workflow
+wf = Workflow.require_workflow workflow
 
 class WorkflowRest < Sinatra::Base
-  get '/' do
-    redirect to(File.join('/', Workflow.workflows.last.to_s))
-  end
+  self
+end.get '/' do
+  redirect to(File.join('/', wf.to_s))
 end
 
 ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
@@ -60,7 +60,7 @@ class WorkflowRest < Sinatra::Base
   use Rack::Deflater
 end
 
-WorkflowRest.add_workflow Workflow.workflows.last, true
+WorkflowRest.add_workflow wf, true
 
 WorkflowRest.port = options[:port] || 4567
 WorkflowRest.bind = options[:bind] || "0.0.0.0"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.21
+  version: 5.13.22
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -264,7 +264,6 @@ files:
 - share/rbbt_commands/workflow/list
 - share/rbbt_commands/workflow/monitor
 - share/rbbt_commands/workflow/prov
-- share/rbbt_commands/workflow/provenance
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove

data/share/rbbt_commands/workflow/provenance

@@ -1,87 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt/workflow'
-
-
-
-require 'rbbt-util'
-require 'fileutils'
-require 'rbbt/util/simpleopt'
-require 'rbbt/workflow/step'
-require 'rbbt/util/misc'
-
-$workdir = Path.setup(File.expand_path(ARGV[0] || '.'))
-
-def info_files
-  $workdir.glob(Step.info_file('**/*'))
-end
-
-def running?(info)
-  Misc.pid_exists? info[:pid]
-end
-
-def job_str(file, info, severity_color = nil)
-  clean_file = file.sub('./','').sub('.info','').gsub('/', Term::ANSIColor.blue(' => '))
-  if $name
-    clean_file
-  else
-    info ||= {:status => :missing_info_file}
-    str = [clean_file, info[:status].to_s] * "\t\t\t[ STATUS = " + " ]" 
-    if info[:status] != :error and info[:status] != :aborted and not info[:status] == :done
-      str += " (#{running?(info)? :running : :dead} #{info[:pid]})" if info[:pid]
-      str += " (children: #{info[:children_pids].collect{|pid| [pid, Misc.pid_exists?(pid) ? "R" : "D"] * ":"} * ", "})" if info.include? :children_pids
-    end
-
-    if severity_color
-      "#{severity_color}" <<  str  << "\033[0m" 
-    else
-      str
-    end
-  end
-end
-
-file = ARGV[0]
-
-deps = {}
-
-$done = []
-def print(file, offset = 1)
-  if not $done.include? file
-    putc "*"
-  end
-
-  step = Step.new file.sub('.info','')
-  
-  info = step.info
-  dependencies = info[:dependencies] || []
-  color = case
-          when (not info)
-            nil
-          when info[:status] == :error 
-            :red
-          when info[:status] == :aborted 
-            :red
-          when (info[:status] != :done and info[:pid] and not running? info)
-            :green
-          end
-
-  puts (" " * offset * 2) << Log.color(color, step.path)
-  $done << file
-  root = File.dirname(File.dirname(file))
-  main_parts = step.path.split "/"
-  dependencies.each do |task,new_file|
-    new_file = File.join(root, task.to_s, new_file)
-    parts = new_file.split "/"
-    common ||= begin
-                 i = 0
-                 parts.each do |p|
-                   break unless main_parts[i] == p
-                   i += 1
-                 end
-                 i
-               end
-    print(new_file[common-1..-1], offset+1)
-  end
-end
-
-print(file)