rbbt-util 5.44.1 → 6.0.3

data/lib/rbbt/workflow/usage.rb

@@ -1,287 +1,289 @@
-require 'rbbt/util/simpleopt'
-
-module Task
-  def doc(workflow = nil, deps = nil)
-    puts Log.color(:yellow, "## #{ name }") << ":"
-    puts "\n" << Misc.format_paragraph(description.strip)  << "\n" if description and not description.empty?
-    puts
-
-    selects = []
-    if inputs.any?
-      inputs.zip(input_types.values_at(*inputs)).select{|i,t| t.to_sym == :select && input_options[i] && input_options[i][:select_options] }.each{|i,t| selects << [i, input_options[i][:select_options]]  }
-      puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
-      puts
-    end
-
-    if deps and deps.any?
-      puts Log.color(:magenta, "Inputs from dependencies:")
-      puts
-      seen = []
-      task_inputs = dep_inputs deps, workflow
-      task_inputs.each do |task,new_inputs|
-        new_inputs.zip(task.input_types.values_at(*new_inputs)).select do |i,t| 
-          t.to_sym == :select && task.input_options.include?(i) && task.input_options[i][:select_options] 
-        end.each do |i,t| 
-          selects << [i, task.input_options[i][:select_options]] 
-        end
-
-        next if new_inputs.empty?
-
-        if task.workflow and task.workflow != workflow
-          puts "  #{Log.color :yellow, ["[#{task.workflow.to_s}]", task.name.to_s] *" "}:"
-        else
-          puts "  #{Log.color :yellow, task.name.to_s}:"
-        end
-        puts unless Log.compact
-        puts SOPT.input_doc(new_inputs, task.input_types, task.input_descriptions, task.input_defaults, true)
-        puts unless Log.compact
-      end
-      puts
-    end
-
-    case
-    when (input_types.values & [:array]).any?
-      puts Log.color(:green, Misc.format_paragraph("Lists are specified as arguments using ',' or '|'. When specified as files the '\\n'
-      also works in addition to the others. You may use the '--array_separator' option
-      the change this default. Whenever a file is specified it may also accept STDIN using
-      the '-' character."))
-      puts
-
-    when (input_types.values & [:text, :tsv]).any?
-      puts Log.color(:green, Misc.format_paragraph("Whenever a file is specified it may also accept STDIN using the '-' character."))
-      puts
-    end
-
-    puts Log.color(:magenta, "Returns: ") << Log.color(:blue, result_type.to_s) << "\n"
-    puts
-
-    if selects.any?
-      puts Log.color(:magenta, "Input select options")
-      puts
-      selects.collect{|p| p}.uniq.each do |input,options|
-        puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| Array === o ? o.first.to_s : o.to_s} * ", ") << "\n"
-        puts unless Log.compact
-      end
-      puts
-    end
-  end
-end
-
-module Workflow
-
-  def dep_tree(name, seen = [])
-    @dep_tree ||= {}
-    @dep_tree[name] ||= begin
-                        dep_tree = {}
-                        self.task_dependencies[name.to_sym].reverse.each do |dep|
-                          next if seen.include? dep
-                          seen << dep
-                          dep = dep.first if Array === dep && dep.length == 1
-                          dep = dep.dependency if DependencyBlock === dep
-
-                          workflow, task = case dep
-                                           when Array
-                                             dep.values_at 0, 1
-                                           when Symbol, String
-                                             [self, dep]
-                                           else
-                                             next
-                                           end
-
-
-                          key = [workflow, task]
-
-                          dep_tree[key] = workflow.dep_tree(task, seen)
-                        end if name && self.task_dependencies[name.to_sym]
-                        dep_tree
-                      end
-  end
-
-  def _prov_tasks(tree)
-    tasks = [] 
-    heap = [tree]
-    while heap.any?
-      t = heap.pop
-      t.each do |k,v|
-        tasks << k
-        heap << v
-      end
-    end
-    tasks
-  end
-
-  def prov_string(tree)
-    description = ""
-
-    last = nil
-    seen = Set.new
-
-    tasks = _prov_tasks(tree)
-    tasks.each do |workflow,task_name|
-
-      next if seen.include?([workflow,task_name])
-
-      child = last && last.include?([workflow, task_name])
-      first = last.nil?
-      last = _prov_tasks(workflow.dep_tree(task_name))
-
-      break if child
-
-      if child
-        description << "->" << task_name.to_s
-      elsif first
-        description << "" << task_name.to_s
-      else
-        description << ";" << task_name.to_s
-      end
-      
-      seen << [workflow, task_name]
-    end
-    description
-  end
-
-  def prov_tree(tree, offset = 0, seen = [])
-
-    return "" if tree.empty?
-
-    lines = []
-
-    offset_str = " " * offset
-
-    lines << offset_str 
-
-    tree.each do |p,dtree| 
-      next if seen.include?(p)
-      seen.push(p)
-      workflow, task = p
-      lines << offset_str + [workflow.to_s, task.to_s] * "#" + "\n" + workflow.prov_tree(dtree, offset + 1, seen)
-    end
-
-    lines * "\n"
-  end
-
-  def doc(task = nil, abridge = false)
-
-    if task.nil?
-      puts Log.color :magenta, self.to_s 
-      puts Log.color :magenta, "=" * self.to_s.length
-
-      if self.documentation[:title] and not self.documentation[:title].empty?
-        puts
-        puts Misc.format_paragraph self.documentation[:title] 
-      end
-
-      if self.documentation[:description] and not self.documentation[:description].empty?
-        puts
-        puts Misc.format_paragraph self.documentation[:description] 
-      end
-      puts
-
-      puts Log.color :magenta, "## TASKS"
-      if self.documentation[:task_description] and not self.documentation[:task_description].empty?
-        puts
-        puts Misc.format_paragraph self.documentation[:task_description] 
-      end
-      puts
-
-      final = Set.new
-      not_final = Set.new
-      tasks.each do |name,task|
-        tree = dep_tree(name)
-        not_final += tree.keys
-        final << name unless not_final.include?(name)
-      end
-
-      not_final.each do |p|
-        final -= [p.last]
-      end
-
-      tasks.each do |name,task|
-        description = task.description || ""
-        description = description.split("\n\n").first
-
-        next if abridge && ! final.include?(name)
-        puts Misc.format_definition_list_item(name.to_s, description, Log.tty_size || 80, 30, :yellow)
-
-        prov_string = prov_string(dep_tree(name))
-        puts Misc.format_paragraph Log.color(:blue, "->" + prov_string) if prov_string && ! prov_string.empty?
-      end
-
-    else
-
-      if Task === task
-        task_name = task.name
-      else
-        task_name = task
-        task = self.tasks[task_name]
-      end
-
-      #dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name[1].to_sym] : self.tasks[dep_name.to_sym]}
-      task.doc(self, self.rec_dependencies(task_name))
-
-      dep_tree = {[self, task_name] => dep_tree(task_name)}
-      prov_tree = prov_tree(dep_tree)
-      if prov_tree && ! prov_tree.empty? && prov_tree.split("\n").length > 2
-
-        puts Log.color :magenta, "## DEPENDENCY GRAPH (abridged)"
-        puts
-        prov_tree.split("\n").each do |line|
-          next if line.strip.empty?
-          if m = line.match(/^( *)(\w+?)#(\w*)/i)
-              offset, workflow, task_name =  m.values_at 1, 2, 3
-            puts [offset, Log.color(:magenta, workflow), "#", Log.color(:yellow, task_name)] * ""
-          else
-            puts Log.color :blue, line 
-          end
-        end
-        puts
-      end
-
-      if self.examples.include? task_name
-        self.examples[task_name].each do |example|
-
-          puts Log.color(:magenta, "Example ") << Log.color(:green, example) + " -- " + Log.color(:blue, example_dir[task_name][example])
-
-          inputs = self.example(task_name, example)
-
-          inputs.each do |input, type, file|
-            case type
-            when :tsv, :array, :text, :file
-              lines = file.read.split("\n")
-              head = lines[0..5].compact * "\n\n"
-              head = head[0..500]
-              puts Misc.format_definition_list_item(input, head, 1000, -1, :blue).gsub(/\n\s*\n/,"\n") 
-              puts '...' if lines.length > 6
-            else
-              puts Misc.format_definition_list_item(input, file.read, Log.tty_size, 20, :blue)
-            end
-          end
-          puts
-        end
-      end
-    end
-  end
-
-  def SOPT_str(task)
-    sopt_options = []
-    self.rec_inputs(task.name).each do |name|
-      short = name.to_s.chars.first
-      boolean = self.rec_input_types(task.name)[name].to_sym == :boolean
-
-      sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
-    end
-
-    sopt_options * ":"
-  end
-
-  def get_SOPT(task)
-    sopt_option_string = self.SOPT_str(task)
-    SOPT.get sopt_option_string
-  end
-
-  def self.get_SOPT(workflow, task)
-    workflow = Workflow.require_workflow workflow if String === workflow
-    task = workflow.tasks[task.to_sym] if String === task || Symbol === task
-    workflow.get_SOPT(task)
-  end
-end
+require_relative '../refactor'
+Rbbt.require_instead 'scout/workflow/usage'
+#require 'rbbt/util/simpleopt'
+#
+#module Task
+#  def doc(workflow = nil, deps = nil)
+#    puts Log.color(:yellow, "## #{ name }") << ":"
+#    puts "\n" << Misc.format_paragraph(description.strip)  << "\n" if description and not description.empty?
+#    puts
+#
+#    selects = []
+#    if inputs.any?
+#      inputs.zip(input_types.values_at(*inputs)).select{|i,t| t.to_sym == :select && input_options[i] && input_options[i][:select_options] }.each{|i,t| selects << [i, input_options[i][:select_options]]  }
+#      puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
+#      puts
+#    end
+#
+#    if deps and deps.any?
+#      puts Log.color(:magenta, "Inputs from dependencies:")
+#      puts
+#      seen = []
+#      task_inputs = dep_inputs deps, workflow
+#      task_inputs.each do |task,new_inputs|
+#        new_inputs.zip(task.input_types.values_at(*new_inputs)).select do |i,t| 
+#          t.to_sym == :select && task.input_options.include?(i) && task.input_options[i][:select_options] 
+#        end.each do |i,t| 
+#          selects << [i, task.input_options[i][:select_options]] 
+#        end
+#
+#        next if new_inputs.empty?
+#
+#        if task.workflow and task.workflow != workflow
+#          puts "  #{Log.color :yellow, ["[#{task.workflow.to_s}]", task.name.to_s] *" "}:"
+#        else
+#          puts "  #{Log.color :yellow, task.name.to_s}:"
+#        end
+#        puts unless Log.compact
+#        puts SOPT.input_doc(new_inputs, task.input_types, task.input_descriptions, task.input_defaults, true)
+#        puts unless Log.compact
+#      end
+#      puts
+#    end
+#
+#    case
+#    when (input_types.values & [:array]).any?
+#      puts Log.color(:green, Misc.format_paragraph("Lists are specified as arguments using ',' or '|'. When specified as files the '\\n'
+#      also works in addition to the others. You may use the '--array_separator' option
+#      the change this default. Whenever a file is specified it may also accept STDIN using
+#      the '-' character."))
+#      puts
+#
+#    when (input_types.values & [:text, :tsv]).any?
+#      puts Log.color(:green, Misc.format_paragraph("Whenever a file is specified it may also accept STDIN using the '-' character."))
+#      puts
+#    end
+#
+#    puts Log.color(:magenta, "Returns: ") << Log.color(:blue, result_type.to_s) << "\n"
+#    puts
+#
+#    if selects.any?
+#      puts Log.color(:magenta, "Input select options")
+#      puts
+#      selects.collect{|p| p}.uniq.each do |input,options|
+#        puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| Array === o ? o.first.to_s : o.to_s} * ", ") << "\n"
+#        puts unless Log.compact
+#      end
+#      puts
+#    end
+#  end
+#end
+#
+#module Workflow
+#
+#  def dep_tree(name, seen = [])
+#    @dep_tree ||= {}
+#    @dep_tree[name] ||= begin
+#                        dep_tree = {}
+#                        self.task_dependencies[name.to_sym].reverse.each do |dep|
+#                          next if seen.include? dep
+#                          seen << dep
+#                          dep = dep.first if Array === dep && dep.length == 1
+#                          dep = dep.dependency if DependencyBlock === dep
+#
+#                          workflow, task = case dep
+#                                           when Array
+#                                             dep.values_at 0, 1
+#                                           when Symbol, String
+#                                             [self, dep]
+#                                           else
+#                                             next
+#                                           end
+#
+#
+#                          key = [workflow, task]
+#
+#                          dep_tree[key] = workflow.dep_tree(task, seen)
+#                        end if name && self.task_dependencies[name.to_sym]
+#                        dep_tree
+#                      end
+#  end
+#
+#  def _prov_tasks(tree)
+#    tasks = [] 
+#    heap = [tree]
+#    while heap.any?
+#      t = heap.pop
+#      t.each do |k,v|
+#        tasks << k
+#        heap << v
+#      end
+#    end
+#    tasks
+#  end
+#
+#  def prov_string(tree)
+#    description = ""
+#
+#    last = nil
+#    seen = Set.new
+#
+#    tasks = _prov_tasks(tree)
+#    tasks.each do |workflow,task_name|
+#
+#      next if seen.include?([workflow,task_name])
+#
+#      child = last && last.include?([workflow, task_name])
+#      first = last.nil?
+#      last = _prov_tasks(workflow.dep_tree(task_name))
+#
+#      break if child
+#
+#      if child
+#        description << "->" << task_name.to_s
+#      elsif first
+#        description << "" << task_name.to_s
+#      else
+#        description << ";" << task_name.to_s
+#      end
+#      
+#      seen << [workflow, task_name]
+#    end
+#    description
+#  end
+#
+#  def prov_tree(tree, offset = 0, seen = [])
+#
+#    return "" if tree.empty?
+#
+#    lines = []
+#
+#    offset_str = " " * offset
+#
+#    lines << offset_str 
+#
+#    tree.each do |p,dtree| 
+#      next if seen.include?(p)
+#      seen.push(p)
+#      workflow, task = p
+#      lines << offset_str + [workflow.to_s, task.to_s] * "#" + "\n" + workflow.prov_tree(dtree, offset + 1, seen)
+#    end
+#
+#    lines * "\n"
+#  end
+#
+#  def doc(task = nil, abridge = false)
+#
+#    if task.nil?
+#      puts Log.color :magenta, self.to_s 
+#      puts Log.color :magenta, "=" * self.to_s.length
+#
+#      if self.documentation[:title] and not self.documentation[:title].empty?
+#        puts
+#        puts Misc.format_paragraph self.documentation[:title] 
+#      end
+#
+#      if self.documentation[:description] and not self.documentation[:description].empty?
+#        puts
+#        puts Misc.format_paragraph self.documentation[:description] 
+#      end
+#      puts
+#
+#      puts Log.color :magenta, "## TASKS"
+#      if self.documentation[:task_description] and not self.documentation[:task_description].empty?
+#        puts
+#        puts Misc.format_paragraph self.documentation[:task_description] 
+#      end
+#      puts
+#
+#      final = Set.new
+#      not_final = Set.new
+#      tasks.each do |name,task|
+#        tree = dep_tree(name)
+#        not_final += tree.keys
+#        final << name unless not_final.include?(name)
+#      end
+#
+#      not_final.each do |p|
+#        final -= [p.last]
+#      end
+#
+#      tasks.each do |name,task|
+#        description = task.description || ""
+#        description = description.split("\n\n").first
+#
+#        next if abridge && ! final.include?(name)
+#        puts Misc.format_definition_list_item(name.to_s, description, Log.tty_size || 80, 30, :yellow)
+#
+#        prov_string = prov_string(dep_tree(name))
+#        puts Misc.format_paragraph Log.color(:blue, "->" + prov_string) if prov_string && ! prov_string.empty?
+#      end
+#
+#    else
+#
+#      if Task === task
+#        task_name = task.name
+#      else
+#        task_name = task
+#        task = self.tasks[task_name]
+#      end
+#
+#      #dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name[1].to_sym] : self.tasks[dep_name.to_sym]}
+#      task.doc(self, self.rec_dependencies(task_name))
+#
+#      dep_tree = {[self, task_name] => dep_tree(task_name)}
+#      prov_tree = prov_tree(dep_tree)
+#      if prov_tree && ! prov_tree.empty? && prov_tree.split("\n").length > 2
+#
+#        puts Log.color :magenta, "## DEPENDENCY GRAPH (abridged)"
+#        puts
+#        prov_tree.split("\n").each do |line|
+#          next if line.strip.empty?
+#          if m = line.match(/^( *)(\w+?)#(\w*)/i)
+#              offset, workflow, task_name =  m.values_at 1, 2, 3
+#            puts [offset, Log.color(:magenta, workflow), "#", Log.color(:yellow, task_name)] * ""
+#          else
+#            puts Log.color :blue, line 
+#          end
+#        end
+#        puts
+#      end
+#
+#      if self.examples.include? task_name
+#        self.examples[task_name].each do |example|
+#
+#          puts Log.color(:magenta, "Example ") << Log.color(:green, example) + " -- " + Log.color(:blue, example_dir[task_name][example])
+#
+#          inputs = self.example(task_name, example)
+#
+#          inputs.each do |input, type, file|
+#            case type
+#            when :tsv, :array, :text, :file
+#              lines = file.read.split("\n")
+#              head = lines[0..5].compact * "\n\n"
+#              head = head[0..500]
+#              puts Misc.format_definition_list_item(input, head, 1000, -1, :blue).gsub(/\n\s*\n/,"\n") 
+#              puts '...' if lines.length > 6
+#            else
+#              puts Misc.format_definition_list_item(input, file.read, Log.tty_size, 20, :blue)
+#            end
+#          end
+#          puts
+#        end
+#      end
+#    end
+#  end
+#
+#  def SOPT_str(task)
+#    sopt_options = []
+#    self.rec_inputs(task.name).each do |name|
+#      short = name.to_s.chars.first
+#      boolean = self.rec_input_types(task.name)[name].to_sym == :boolean
+#
+#      sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
+#    end
+#
+#    sopt_options * ":"
+#  end
+#
+#  def get_SOPT(task)
+#    sopt_option_string = self.SOPT_str(task)
+#    SOPT.get sopt_option_string
+#  end
+#
+#  def self.get_SOPT(workflow, task)
+#    workflow = Workflow.require_workflow workflow if String === workflow
+#    task = workflow.tasks[task.to_sym] if String === task || Symbol === task
+#    workflow.get_SOPT(task)
+#  end
+#end

data/lib/rbbt/workflow/util/archive.rb

@@ -28,7 +28,7 @@ class Step
       seen = Set.new
       while deps.any?
         path = deps.shift
-        dep = Workflow.load_step path
+        dep = Step.load path
         seen << dep.path
         dep.dependencies.each do |dep|
           next if seen.include? dep.path
@@ -83,10 +83,10 @@ class Step
       while deps.any?
         path = deps.shift
 
-        dep = Workflow.load_step path
+        dep = Step.load path
         seen << dep.path
 
-        dep.load_dependencies_from_info
+        #dep.load_dependencies_from_info
 
         dep.dependencies.each do |dep|
           next if seen.include? dep.path
@@ -96,7 +96,7 @@ class Step
       end
 
       rec_dependencies.each do |path|
-        dep = Workflow.load_step path
+        dep = Workflow.load_step path.dup
         job_files << dep.path
         job_files << dep.files_dir if Dir.glob(dep.files_dir + '/*').any?
         job_files << dep.info_file if File.exist?(dep.info_file)
@@ -120,7 +120,8 @@ class Step
         if File.directory?(target)
           CMD.cmd_log("rsync #{MAIN_RSYNC_ARGS} --copy-unsafe-links '#{ tmpdir }/' '#{ target }/'")
         else
-          CMD.cmd_log("tar cvhzf '#{target}'  ./*")
+          Misc.tarize('.', target)
+          #CMD.cmd_log("tar cvhzf '#{target}'  ./*")
         end
       end
       Log.debug "Archive finished at: #{target}"

data/lib/rbbt/workflow/util/data.rb

@@ -3,7 +3,7 @@ require 'rbbt/workflow/examples'
 
 module Workflow
   module Data
-    class DataNotFound < RbbtException; end
+    class DataNotFound < ScoutException; end
 
     def data_dir(directory)
       @@data_directory = directory