rbbt-util 5.29.0 → 5.29.1

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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@@ -3,6 +3,7 @@ module HPC
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  module SLURM
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  def self.orchestrate_job(job, options, seen = {})
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  return if job.done?
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+ return unless job.path.split("/")[-4] == "jobs"
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  options.delete "recursive_clean"
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  options.delete "tail"
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  rules = YAML.load(Open.read(options[:rules])) if options[:rules]
@@ -494,6 +494,7 @@ EOF
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  dry_run = options.delete :dry_run
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  tail = options.delete :tail
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  dependencies = options.delete :slurm_dependencies
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+ options[:jobname] = job.clean_name
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  workflow = job.workflow
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@@ -518,7 +519,6 @@ EOF
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  inputs_dir = File.join(tmp_directory, 'inputs_dir')
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  saved = Step.save_job_inputs(job, inputs_dir)
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-
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  if saved && saved.any?
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  options[:inputs_dir] = inputs_dir
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  cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
@@ -287,7 +287,9 @@ module Misc
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  when Symbol
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  obj.to_s
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  when (defined?(Path) and Path)
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- if Step === obj.resource
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+ if defined?(Step) && Open.exists?(Step.info_file(obj))
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+ obj2str(Workflow.load_step(obj))
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+ elsif defined?(Step) && Step === obj.resource
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  "Step file: " + obj
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  else
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  if obj.exists?
@@ -322,7 +324,11 @@ module Misc
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  remove_long_items(obj)
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  when File
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  if obj.respond_to? :filename and obj.filename
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- "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
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+ if defined?(Step) && Open.exists?(Step.info_file(obj.filename))
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+ obj2str(Workflow.load_step(obj.filename))
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+ else
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+ "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
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+ end
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  else
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  "<IO:" << obj.path << "--" << mtime_str(obj.path) << ">"
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  end
@@ -330,7 +336,11 @@ module Misc
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  "<IO:" << obj.short_path << ">"
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  when IO
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  if obj.respond_to? :filename and obj.filename
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- "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
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+ if defined?(Step) && Open.exists?(Step.info_file(obj.filename))
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+ obj2str(Workflow.load_step(obj.filename))
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+ else
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+ "<IO:" << obj.filename << "--" << mtime_str(obj.filename) << ">"
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+ end
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  else
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  if obj.respond_to? :obj2str
@@ -16,6 +16,10 @@ end
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  module Workflow
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+ def self.job_path?(path)
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+ path.split("/")[-4] == "jobs"
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+ end
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+
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  def log(status, message = nil, &block)
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  Step.log(status, message, nil, &block)
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  end
@@ -301,8 +305,9 @@ module Workflow
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  def setup_override_dependency(dep, workflow, task_name)
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  dep = Step === dep ? dep : Workflow.load_step(dep)
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+ dep.workflow = workflow
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  dep.info[:name] = dep.name
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- dep.original_task_name ||= dep.task_name
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+ dep.original_task_name ||= dep.task_name if dep.workflow
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  begin
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  workflow = Kernel.const_get workflow if String === workflow
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  dep.task = workflow.tasks[task_name] if dep.task.nil? && workflow.tasks.include?(task_name)
@@ -94,17 +94,21 @@ class Step
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  Log.debug "Saving job input #{name} (#{type}) into #{path}"
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  case
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  when Step === value
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- Open.link(value.path, path)
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+ Open.ln_s(value.path, path)
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  when type.to_s == "file"
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  if String === value && File.exists?(value)
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- Open.link(value, path)
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+ Open.ln_s(value, path)
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  else
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  Open.write(path + '.yaml', value.to_yaml)
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  end
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  when Array === value
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- Open.write(path, value * "\n")
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+ Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
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  when IO === value
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- Open.write(path, value)
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+ if value.filename && String === value.filename && File.exists?(value.filename)
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+ Open.ln_s(value.filename, path)
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+ else
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+ Open.write(path, value)
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+ end
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  else
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  Open.write(path, value.to_s)
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  end
@@ -117,13 +121,17 @@ class Step
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  task_name = Symbol === job.overriden ? job.overriden : job.task_name
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  workflow = job.workflow
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  workflow = Kernel.const_get workflow if String === workflow
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- task_info = workflow.task_info(task_name)
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- input_types = task_info[:input_types]
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- task_inputs = task_info[:inputs]
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- input_defaults = task_info[:input_defaults]
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+ if workflow
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+ task_info = workflow.task_info(task_name)
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+ input_types = task_info[:input_types]
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+ task_inputs = task_info[:inputs]
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+ input_defaults = task_info[:input_defaults]
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+ else
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+ task_info = input_types = task_inputs = input_defaults = {}
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+ end
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  inputs = {}
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- real_inputs = job.real_inputs || job.info[:real_inputs]
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+ real_inputs = job.real_inputs || job.info[:real_inputs]
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  job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
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  next unless task_inputs.include? name.to_sym
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  next unless real_inputs.include? name.to_sym
@@ -103,7 +103,7 @@ class Step
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  end
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  job.dup_inputs unless status == 'done' or job.started?
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- job.init_info(status == 'noinfo') unless status == 'waiting' || status == 'done' || job.started?
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+ job.init_info(status == 'noinfo') unless status == 'waiting' || status == 'done' || job.started? || ! Workflow.job_path?(job.path)
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  canfail = ComputeDependency === job && job.canfail?
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  end
@@ -130,7 +130,6 @@ class Step
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  (inputs.flatten.select{|i| Step === i} + inputs.flatten.select{|dep| Path === dep && Step === dep.resource}.collect{|dep| dep.resource})
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  end
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-
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  def execute_dependency(dependency, log = true)
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  task_name = self.task_name
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  canfail_paths = self.canfail_paths
@@ -122,7 +122,6 @@ class Step
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  reject{|dependency| (defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === dependency) || Open.remote?(dependency.path) }.
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  reject{|dependency| dependency.error? }.
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  #select{|dependency| Open.exists?(dependency.path) || ((Open.exists?(dependency.info_file) && (dependency.status == :cleaned) || dependency.status == :waiting)) }.
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- #select{|dependency| Open.exists?(dependency.path) || ((Open.exists?(dependency.info_file) && (dependency.status == :cleaned) || dependency.status == :waiting)) }.
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  select{|dependency| dependency.updatable? }.
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  collect{|dependency| Workflow.relocate_dependency(self, dependency)}
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  end
@@ -22,11 +22,14 @@ class Step
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  end
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  def self.prov_report_msg(status, name, path, info = nil)
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- parts = path.sub(/\{.*/,'').sub(/#{Regexp.quote(name)}$/,'').split "/"
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+ parts = path.sub(/\{.*/,'').split "/"
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+ parts.pop
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+
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  task = Log.color(:yellow, parts.pop)
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  workflow = Log.color(:magenta, parts.pop)
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- if status.to_s == 'noinfo' and parts.last != 'jobs'
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+ #if status.to_s == 'noinfo' && parts.last != 'jobs'
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+ if ! Workflow.job_path?(path)
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  task, status, workflow = Log.color(:yellow, info[:task_name]), Log.color(:green, "file"), Log.color(:magenta, "-")
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  end
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@@ -386,9 +386,9 @@ class TestWorkflow < Test::Unit::TestCase
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  job.run
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  Misc.with_env "RBBT_UPDATE", 'true' do
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  assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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- job = TestWF.job(:t3)
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- job.step(:t1).clean
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- assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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+ #job = TestWF.job(:t3)
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+ #job.step(:t1).clean
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+ #assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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  job = TestWF.job(:t3).recursive_clean
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  job.run
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  assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
@@ -427,7 +427,7 @@ class TestWorkflow < Test::Unit::TestCase
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  TmpFile.with_file do |dir|
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  Path.setup(dir)
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  Step.save_job_inputs(job, dir)
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- assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.read']
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+ assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.yaml']
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  inputs = Workflow.load_inputs(dir, [:file], :file => :file)
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  assert_equal inputs, {:file => 'code'}
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  end
@@ -455,9 +455,9 @@ class TestWorkflow < Test::Unit::TestCase
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  job.run
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  Misc.with_env "RBBT_UPDATE", 'true' do
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  assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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- job = TestWF.job(:t3)
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- job.step(:t1).clean
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- assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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+ #job = TestWF.job(:t3)
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+ #job.step(:t1).clean
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+ #assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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  job = TestWF.job(:t3).recursive_clean
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  job.run
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  assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-util
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  version: !ruby/object:Gem::Version
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- version: 5.29.0
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+ version: 5.29.1
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2021-01-12 00:00:00.000000000 Z
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+ date: 2021-01-14 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake