rbbt-util 5.5.58 → 5.5.59

checksums.yaml

@@ -1,15 +1,15 @@
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   metadata.gz: !binary |-
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   data.tar.gz: !binary |-
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+    NDNlMTU0Y2JhMjcwMzlmYjkwMmY0NWU0OGJmODVlZDRmODdkZjVkZg==
 SHA512:
   metadata.gz: !binary |-
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+    ZjhkODIwN2Y4YzJiMDMxODVlZWZiZTIxMjcwOGZiMTM5MmU0MDQ=

data/lib/rbbt/persist/tsv.rb

@@ -8,7 +8,7 @@ module Persist
   TC_CONNECTIONS = {}
 
   def self.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB)
-    write = true if not File.exists?(path)
+    write = true unless File.exists? path
 
     tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB"
     tokyocabinet_class = TokyoCabinet::BDB if tokyocabinet_class == "BDB"

data/lib/rbbt/tsv/accessor.rb

@@ -1,4 +1,5 @@
 require 'yaml'
+require 'rbbt/annotations'
 module TSV
 
   TSV_SERIALIZER = YAML
@@ -248,6 +249,7 @@ module TSV
 
   def sort_by(field = nil, just_keys = false, &block)
     field = :all if field.nil?
+
     if field == :all
       elems = collect
     else
@@ -298,9 +300,8 @@ module TSV
           end
         end
         if just_keys
-          #keys = elems.sort_by{|key, value| value }.collect{|key, value| key}
           keys = sorted.collect{|key, value| key}
-          keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true))
+          keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true)) unless @unnamed
           keys
         else
           sorted.collect{|key, value| [key, self[key]]}
@@ -308,7 +309,9 @@ module TSV
       end
     else
       if just_keys
-        elems.sort_by(&block).collect{|key, value| key}
+        keys = elems.sort_by(&block).collect{|key, value| key}
+        keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true)) unless @unnamed
+        keys
       else
         elems.sort_by(&block).collect{|key, value| [key, self[key]]}
       end

data/lib/rbbt/tsv/manipulate.rb

@@ -414,7 +414,7 @@ module TSV
       case
       when (Array === method and (key == :key or key_field == key))
         with_unnamed do
-          Annotated.purge(method).sort.uniq.each{|key| 
+          Annotated.purge(method).uniq.each{|key| 
             new[key] = self[key] if invert ^ (self.include? key)
           }
         end

data/lib/rbbt/util/color.rb

@@ -30,6 +30,25 @@ class Color
   # Default value for #darken, #lighten etc.
   BRIGHTNESS_DEFAULT = 0.2
 
+  SOLARIZED = {
+    :base03 =>     '#002b36',
+    :base02 =>     '#073642',
+    :base01 =>     '#586e75',
+    :base00 =>     '#657b83',
+    :base0 =>      '#839496',
+    :base1 =>      '#93a1a1',
+    :base2 =>      '#eee8d5',
+    :base3 =>      '#fdf6e3',
+    :yellow =>     '#b58900',
+    :orange =>     '#cb4b16',
+    :red =>        '#dc322f',
+    :magenta =>    '#d33682',
+    :violet =>     '#6c71c4',
+    :blue =>       '#268bd2',
+    :cyan =>       '#2aa198',
+    :green =>      '#859900',
+  }
+
   # Constructor.  Inits to white (#FFFFFF) by default, or accepts any params
   # supported by #parse.
   def initialize(*args)

data/lib/rbbt/util/log.rb

@@ -1,4 +1,8 @@
+require 'term/ansicolor'
+require 'rbbt/util/color'
+
 module Log
+  extend Term::ANSIColor
 
   DEBUG    = 0
   LOW      = 1
@@ -17,21 +21,24 @@ module Log
     @logfile = nil
   end
 
-  WHITE, DARK, GREEN, YELLOW, RED = ["0;37m", "0m", "0;32m", "0;33m", "0;31m"].collect{|e| "\033[#{e}"}
+  WHITE, DARK, GREEN, YELLOW, RED = Color::SOLARIZED.values_at :base0, :base00, :green, :yellow, :magenta
+
+  SEVERITY_COLOR = [reset, green, yellow, red, green, yellow, red] #.collect{|e| "\033[#{e}"}
 
-  SEVERITY_COLOR = [WHITE, GREEN, YELLOW, RED, GREEN, YELLOW, ERROR].collect{|e| "\033[#{e}"}
+  HIGHLIGHT = "\033[1m"
 
   def self.log(message = nil, severity = MEDIUM, &block)
-    message ||= block
+    return if severity < self.severity
+    message ||= block.call if block_given?
     return if message.nil?
+
     severity_color = SEVERITY_COLOR[severity]
-    font_color = {true => WHITE, false => DARK}[severity >= INFO]
+    time = Time.now.strftime("%m/%d/%y-%H:%M:%S")
 
-    return if severity < self.severity
-    message = message.call if Proc === message
-    return if message.nil? or message.empty?
+    prefix = time << "[" << severity_color << severity.to_s << SEVERITY_COLOR[0] << "]"
+    message = "" << HIGHLIGHT << message << SEVERITY_COLOR[0] if severity >= INFO
+    str = prefix << " " << message
 
-    str = "\033[0;37m#{Time.now.strftime("[%m/%d/%y-%H:%M:%S]")}#{severity_color}[#{severity.to_s}]\033[0m:#{font_color} " <<  message.strip  << "\033[0m"
     STDERR.puts str
     logfile.puts str unless logfile.nil?
   end

data/lib/rbbt/util/simpleopt.rb

@@ -1,74 +1,77 @@
 module SOPT
+
+  #{{{ ACCESSORS
+  
   class << self
     attr_accessor :command, :summary, :synopsys, :description
     attr_accessor :inputs, :input_shortcuts, :input_types, :input_descriptions, :input_defaults
+  end
 
-    def command
-      @command ||= File.basename($0)
-    end
+  def self.command
+    @command ||= File.basename($0)
+  end
 
-    def summary
-      @summary ||= ""
-    end
+  def self.summary
+    @summary ||= ""
+  end
 
-    def synopsys
-      @synopsys ||= begin
-                      "#{command} " <<
-                      inputs.collect{|name|
-                        "[" << input_format(name, input_types[name] || :string, input_defaults[name], input_shortcuts[name]).sub(/:$/,'') << "]"
-                      } * " "
-                    end
-    end
+  def self.synopsys
+    @synopsys ||= begin
+                    "#{command} " <<
+                    inputs.collect{|name|
+                      "[" << input_format(name, input_types[name] || :string, input_defaults[name], input_shortcuts[name]).sub(/:$/,'') << "]"
+                    } * " "
+                  end
+  end
 
-    def description
-      @description ||= "Missing"
-    end
+  def self.description
+    @description ||= "Missing"
+  end
 
 
-    def shortcuts
-      @shortcuts ||= []
-    end
+  def self.shortcuts
+    @shortcuts ||= []
+  end
 
-    def all
-      @all ||= {}
-    end
-    
-    def inputs 
-      @inputs ||= []
-    end
+  def self.all
+    @all ||= {}
+  end
   
-    def input_shortcuts 
-      @input_shortcuts ||= {}
-    end
+  def self.inputs 
+    @inputs ||= []
+  end
 
-    def input_types 
-      @input_types ||= {}
-    end
- 
-    def input_descriptions 
-      @input_descriptions ||= {}
-    end
- 
-    def input_defaults 
-      @input_defaults ||= {}
-    end
+  def self.input_shortcuts 
+    @input_shortcuts ||= {}
+  end
 
+  def self.input_types 
+    @input_types ||= {}
+  end
 
-    def reset
-      @shortcuts = []
-      @all = {}
-    end
+  def self.input_descriptions 
+    @input_descriptions ||= {}
+  end
 
-    def record(info)
-      input = info[:long].sub("--", '')
-      inputs << input
-      input_types[input] = info[:arg] ? :string : :boolean
-      input_descriptions[input] = info[:description]
-      input_defaults[input] = info[:default]
-      input_shortcuts[input] = info[:short]? info[:short].sub("-",'') : nil
-    end
+  def self.input_defaults 
+    @input_defaults ||= {}
   end
 
+  def self.reset
+    @shortcuts = []
+    @all = {}
+  end
+
+  #{{{ PARSING
+  
+  def self.record(info)
+    input = info[:long].sub("--", '')
+    inputs << input
+    input_types[input] = info[:arg] ? :string : :boolean
+    input_descriptions[input] = info[:description]
+    input_defaults[input] = info[:default]
+    input_shortcuts[input] = info[:short]? info[:short].sub("-",'') : nil
+  end
 
   def self.short_for(name)
     short = []
@@ -84,60 +87,6 @@ module SOPT
     short * ""
   end
 
-  def self.input_format(name, type = nil, default = nil, short = "")
-    short = short_for(name) if not short.nil? and short.empty?
-
-    input_str = short.nil? ? "--#{name}" : "-#{short}, --#{name}"
-    input_str << case type
-    when nil
-      "#{default != nil ? " (default '#{default}')" : ""}:"
-    when :boolean
-      "[=false]#{default != nil ? " (default '#{default}')" : ""}:"
-    when :tsv, :text
-      "=<filename.#{type}|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
-    when :array
-      "=<string[,string]*|filename.list|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
-    else
-      "=<#{ type }>#{default != nil ? " (default '#{default}')" : ""}:"
-    end
-  end
-
-  def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
-    type = description = default = nil
-    shortcut = ""
-    inputs.collect do |name|
-
-      type = input_types[name] unless input_types.nil?
-      description = input_descriptions[name] unless input_descriptions.nil?
-      default = input_defaults[name] unless input_defaults.nil?
-      shortcut = input_shortcuts[name] unless input_shortcuts.nil?
-
-      type = :string if type.nil?
-
-      str  = "  * " << SOPT.input_format(name, type.to_sym, default, shortcut) << "\n"
-      str << "    " << description << "\n" if description and not description.empty?
-      str
-    end * "\n"
-  end
-
-  def self.doc
-    doc = <<-EOF
-#{command}(1) -- #{summary}
-#{"=" * (command.length + summary.length + 7)}
-
-## SYNOPSYS
-
-#{synopsys}
-
-## DESCRIPTION
-
-#{description}
-
-## OPTIONS
-
-#{input_doc(inputs, input_types, input_descriptions, input_defaults, input_shortcuts)}
-    EOF
-  end
 
   def self.name(info)
     (info[:long] || info[:short]).sub(/^-*/,'')
@@ -225,4 +174,61 @@ module SOPT
 
     options
   end
+
+  #{{{ DOCUMENTATION
+
+  def self.input_format(name, type = nil, default = nil, short = "")
+    short = short_for(name) if not short.nil? and short.empty?
+
+    input_str = short.nil? ? "--#{name}" : "-#{short}, --#{name}"
+    input_str << case type
+    when nil
+      "#{default != nil ? " (default '#{default}')" : ""}:"
+    when :boolean
+      "[=false]#{default != nil ? " (default '#{default}')" : ""}:"
+    when :tsv, :text
+      "=<filename.#{type}|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+    when :array
+      "=<string[,string]*|filename.list|->#{default != nil ? " (default '#{default}')" : ""}; Use '-' for STDIN:"
+    else
+      "=<#{ type }>#{default != nil ? " (default '#{default}')" : ""}:"
+    end
+  end
+
+  def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
+    type = description = default = nil
+    shortcut = ""
+    inputs.collect do |name|
+
+      type = input_types[name] unless input_types.nil?
+      description = input_descriptions[name] unless input_descriptions.nil?
+      default = input_defaults[name] unless input_defaults.nil?
+      shortcut = input_shortcuts[name] unless input_shortcuts.nil?
+
+      type = :string if type.nil?
+
+      str  = "  * " << SOPT.input_format(name, type.to_sym, default, shortcut) << "\n"
+      str << "    " << description << "\n" if description and not description.empty?
+      str
+    end * "\n"
+  end
+
+  def self.doc
+    doc = <<-EOF
+#{command}(1) -- #{summary}
+#{"=" * (command.length + summary.length + 7)}
+
+## SYNOPSYS
+
+#{synopsys}
+
+## DESCRIPTION
+
+#{description}
+
+## OPTIONS
+
+#{input_doc(inputs, input_types, input_descriptions, input_defaults, input_shortcuts)}
+    EOF
+  end
 end

data/lib/rbbt/workflow.rb

@@ -5,33 +5,16 @@ require 'rbbt/workflow/accessor'
 
 module Workflow
 
-  class << self
-    attr_accessor :autoinstall
-
-    def autoinstall
-      @autoload ||= ENV["RBBT_WORKFLOW_AUTOINSTALL"] == "true"
-    end
-  end
-
-  def self.resolve_locals(inputs)
-    inputs.each do |name, value|
-      if value =~ /^local:(.*?):(.*)/ or 
-        (Array === value and value.length == 1 and value.first =~ /^local:(.*?):(.*)/) or
-        (TSV === value and value.size == 1 and value.keys.first =~ /^local:(.*?):(.*)/)
-        task_name = $1
-        jobname = $2
-        value = load_id(File.join(task_name, jobname)).load
-      end
-      inputs[name] = value
-    end 
-  end
-
   #{{{ WORKFLOW MANAGEMENT 
   class << self
-    attr_accessor :workflows
+    attr_accessor :workflows, :autoinstall
   end
+
   self.workflows = []
 
+  def self.autoinstall
+    @autoload ||= ENV["RBBT_WORKFLOW_AUTOINSTALL"] == "true"
+  end
   def self.extended(base)
     self.workflows << base
     base.libdir = Path.caller_lib_dir.tap{|p| p.resource = base}
@@ -185,10 +168,25 @@ module Workflow
   end
 
   # {{{ JOB MANAGEMENT
+  DEFAULT_NAME="Default"
+
+  def self.resolve_locals(inputs)
+    inputs.each do |name, value|
+      if value =~ /^local:(.*?):(.*)/ or 
+        (Array === value and value.length == 1 and value.first =~ /^local:(.*?):(.*)/) or
+        (TSV === value and value.size == 1 and value.keys.first =~ /^local:(.*?):(.*)/)
+        task_name = $1
+        jobname = $2
+        value = load_id(File.join(task_name, jobname)).load
+        inputs[name] = value
+      end
+    end 
+  end
 
   def job(taskname, jobname = nil, inputs = {})
     taskname = taskname.to_sym
-    jobname = "Default" if jobname.nil? or jobname.empty?
+    jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?
+
     task = tasks[taskname]
     raise "Task not found: #{ taskname }" if task.nil?
 
@@ -244,6 +242,7 @@ module Workflow
     }
   end
 
+  #{{{ Make workflow resources local
   def local_persist_setup
     class << self
       include LocalPersist

data/lib/rbbt/workflow/accessor.rb

@@ -6,7 +6,7 @@ class Step
   INFO_SERIALIAZER = Marshal
 
   def name
-    @path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1')
+    path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1')
   end
 
   def clean_name
@@ -21,7 +21,7 @@ class Step
 
   def info_file
     @info_file ||= begin
-                     @path.nil? ? nil : @path + '.info'
+                     path.nil? ? nil : path + '.info'
                    end
   end
 
@@ -110,7 +110,7 @@ class Step
   # {{{ INFO
 
   def files_dir
-    @path + '.files'
+    path + '.files'
   end
 
   def files
@@ -275,19 +275,21 @@ module Workflow
 
   TAG = :hash
   def step_path(taskname, jobname, inputs, dependencies)
-    raise "Jobname makes an invalid path: #{ jobname }" if jobname =~ /\.\./
-    if inputs.any? or dependencies.any?
-      tagged_jobname = case TAG
-                       when :hash
-                         jobname + '_' + Misc.digest((inputs * "\n" + ";" + dependencies.collect{|dep| dep.name} * "\n"))
-                       else
-                         jobname
-                       end
-    else
-      tagged_jobname = jobname
-    end
+    Proc.new{
+      raise "Jobname makes an invalid path: #{ jobname }" if jobname =~ /\.\./
+      if inputs.any? or dependencies.any?
+        tagged_jobname = case TAG
+                         when :hash
+                           jobname + '_' + Misc.digest((inputs * "\n" + ";" + dependencies.collect{|dep| dep.name} * "\n"))
+                         else
+                           jobname
+                         end
+      else
+        tagged_jobname = jobname
+      end
 
-    workdir[taskname][tagged_jobname].find
+      workdir[taskname][tagged_jobname].find
+    }
   end
 
 

data/lib/rbbt/workflow/definition.rb

@@ -4,7 +4,6 @@ require 'rbbt/workflow/annotate'
 module Workflow
   include AnnotatedModule
 
-
   AnnotatedModule.add_consummable_annotation(self,
                                              :result_description => "",
                                              :result_type        => nil,

data/lib/rbbt/workflow/step.rb

@@ -14,8 +14,8 @@ class Step
   class Aborted < Exception; end
 
   def initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil)
-    path = Misc.sanitize_filename path
-    @path = Path.setup(path)
+    path = Path.setup(Misc.sanitize_filename(path)) if String === path
+    @path = path
     @task = task
     @bindings = bindings
     @dependencies = case
@@ -29,6 +29,11 @@ class Step
     @inputs = inputs || []
   end
 
+  def path
+    @path = Misc.sanitize_filename(Path.setup(@path.call)) if Proc === @path
+    @path
+  end
+
   class << self
     attr_accessor :log_relay_step
   end
@@ -88,7 +93,7 @@ class Step
   end
 
   def run(no_load = false)
-    result = Persist.persist "Job", @task.result_type, :file => @path, :check => rec_dependencies.collect{|dependency| dependency.path }.uniq, :no_load => no_load do
+    result = Persist.persist "Job", @task.result_type, :file => path, :check => rec_dependencies.collect{|dependency| dependency.path }.uniq, :no_load => no_load do
       @exec = false
       if Step === Step.log_relay_step and not self == Step.log_relay_step
         relay_log(Step.log_relay_step) unless self.respond_to? :relay_step and self.relay_step
@@ -177,11 +182,11 @@ class Step
         begin
           run(true)
         rescue Step::Aborted
-          Log.debug{"Forked process aborted: #{@path}"}
+          Log.debug{"Forked process aborted: #{path}"}
           log :aborted, "Aborted"
           raise $!
         rescue Exception
-          Log.debug("Exception caught on forked process: #{@path}")
+          Log.debug("Exception caught on forked process: #{path}")
           raise $!
         end
 

data/test/rbbt/workflow/test_step.rb

@@ -1,11 +1,12 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
 require 'rbbt/workflow/task'
 require 'rbbt/workflow/step'
+require 'rbbt/tsv'
 require 'rbbt'
 
 class TestStep < Test::Unit::TestCase
 
-  def test_step
+  def _test_step
     task  = Task.setup do "TEST" end
     task2  = Task.setup do raise "Persistence ignored" end
     TmpFile.with_file do |tmp|
@@ -17,7 +18,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_dependency
+  def _test_dependency
     str = "TEST"
     str2 = "TEST2"
     TmpFile.with_file do |tmpfile|
@@ -46,7 +47,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_dependency_log_relay
+  def _test_dependency_log_relay
     str = "TEST"
     TmpFile.with_file do |tmpfile|
       task1  = Task.setup :result_type => nil, :name => :task1 do 
@@ -65,7 +66,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_log_relay_step
+  def _test_log_relay_step
     str = "TEST"
     TmpFile.with_file do |tmpfile|
       task1  = Task.setup :result_type => nil, :name => :task1 do 
@@ -87,7 +88,7 @@ class TestStep < Test::Unit::TestCase
   end
 
 
-  def test_exec
+  def _test_exec
     TmpFile.with_file do |lock|
       task  = Task.setup do "TEST" end
       TmpFile.with_file do |tmp|
@@ -98,7 +99,7 @@ class TestStep < Test::Unit::TestCase
   end
 
 
-  def test_fork
+  def _test_fork
     TmpFile.with_file do |lock|
       task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
       TmpFile.with_file do |tmp|
@@ -114,7 +115,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_abort
+  def _test_abort
     TmpFile.with_file do |lock|
       task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
       TmpFile.with_file do |tmp|
@@ -131,7 +132,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_files
+  def _test_files
     TmpFile.with_file do |lock|
       task  = Task.setup do 
         Open.write(file("test"),"TEST")
@@ -145,7 +146,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_messages
+  def _test_messages
     TmpFile.with_file do |lock|
       task  = Task.setup do 
         message "WRITE"
@@ -161,7 +162,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_subdir
+  def _test_subdir
     TmpFile.with_file do |lock|
       task  = Task.setup do 
         message "WRITE"
@@ -178,7 +179,7 @@ class TestStep < Test::Unit::TestCase
     end
   end
 
-  def test_semaphore
+  def _test_semaphore
     TmpFile.with_file do |semaphore|
       begin
         semaphore = "/" << semaphore.gsub('/','_')
@@ -210,5 +211,4 @@ class TestStep < Test::Unit::TestCase
 
   end
 
-
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.58
+  version: 5.5.59
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -94,6 +94,20 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: term-ansicolor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: ZenTest
   requirement: !ruby/object:Gem::Requirement