rbbt-util 5.44.1 → 6.0.4

data/lib/rbbt/tsv.rb

@@ -1,208 +1,210 @@
-require 'rbbt/persist'
-require 'rbbt/persist/tsv'
-
-require 'rbbt/util/log'
-require 'rbbt/util/misc'
-require 'rbbt/util/named_array'
-
-require 'rbbt/tsv/util'
-require 'rbbt/tsv/serializers'
-require 'rbbt/tsv/parser'
-require 'rbbt/tsv/accessor'
-require 'rbbt/tsv/manipulate'
-require 'rbbt/tsv/index'
-require 'rbbt/tsv/attach'
-require 'rbbt/tsv/filter'
-require 'rbbt/tsv/field_index'
-require 'rbbt/tsv/parallel'
-require 'rbbt/tsv/stream'
-require 'rbbt/tsv/melt'
-require 'rbbt/tsv/matrix'
-require 'rbbt/tsv/marshal'
-
-module TSV
-  class << self
-    attr_accessor :lock_dir, :unnamed
-    
-    def lock_dir
-      @lock_dir ||= Rbbt.tmp.tsv_open_locks.find
-    end
-  end
-
-  def self.str2options(str)
-    field_options,_sep, rest =  str.partition("#")
-    key, fields_str = field_options.split("~")
-
-    fields = fields_str.nil? ? [] : fields_str.split(/,\s*/)
-
-    rest = ":type=" << rest if rest =~ /^:?\w+$/
-    rest_options = rest.nil? ? {} : Misc.string2hash(rest)
-
-    {:key_field => key, :fields => fields}.merge(rest_options)
-  end
-
-  def self.setup(hash, type = nil, options = nil)
-    type, options = nil, type if options.nil? and (Hash === type or (String === type and type.include? "~"))
-    options = TSV.str2options(options) if String === options and options.include? "~"
-    options ||= {}
-    options[:type] ||= type unless type.nil?
-
-    options = Misc.add_defaults options, :default_value => [], :unnamed => TSV.unnamed
-    default_value = Misc.process_options options, :default_value
-    hash = Misc.array2hash(hash, default_value) if Array === hash
-    hash.extend TSV
-
-    IndiferentHash.setup(options)
-    ENTRIES.each do |entry|
-      hash.send("#{ entry }=", options[entry.to_s]) if options.include? entry.to_s
-      hash.send("#{ entry }=", options[entry.to_sym]) if options.include? entry.to_sym
-    end
-
-    hash.unnamed = options[:unnamed]
-
-    hash
-  end
-
-  # options shift if type.nil?
-  def self.open(source, type = nil, options = nil)
-    type, options = nil, type if options.nil? and (Hash === type or (String === type and type.include? "~"))
-    options = TSV.str2options(options) if String === options and options.include? "~"
-    options ||= {}
-    options[:type] ||= type unless type.nil?
-    options[:zipped] = true if options[:one2one]
-
-    persist_options = Misc.pull_keys options, :persist
-
-    raise "TSV source is nil" if source.nil?
-
-    filename = get_filename source
-    serializer = Misc.process_options options, :serializer
-    unnamed = Misc.process_options options, :unnamed
-    entity_options = Misc.process_options options, :entity_options
-
-
-    Log.debug "TSV open: #{ filename } - #{Misc.fingerprint options }.#{unnamed ? " [unnamed]" : "[not unnamed]"}"
-
-    data = nil
-
-    lock_filename = filename.nil? ? nil : Persist.persistence_path(filename + '.open', {:dir => TSV.lock_dir})
-    Misc.lock lock_filename  do
-      data = Persist.persist_tsv source, filename, options, persist_options do |data|
-        if serializer
-          data.extend TSV unless TSV === data
-          data.serializer = serializer
-        end
-
-        tsv_grep = Misc.process_options options, :tsv_grep
-        tsv_grep ||= Misc.process_options options, :grep
-        open_options = Misc.pull_keys options, :open
-
-        stream = get_stream source, options.merge(open_options)
-        parse stream, data, options.merge(:tsv_grep => tsv_grep)
-
-        if ! open_options[:noclose]
-          stream.close unless stream.closed?
-          stream.join if stream.respond_to?(:join)
-        end
-
-        data.filename = filename.to_s unless filename.nil?
-
-        if data.identifiers.nil? and Path === filename and filename.identifier_file_path
-          data.identifiers = filename.identifier_file_path.find if filename.identifier_file_path.exists?
-        end
-
-        data
-      end
-    end
-
-
-    data.unnamed = unnamed unless unnamed.nil?
-
-    data.entity_options = entity_options
-
-    if Path === source && data.identifiers
-      Path.setup(data.identifiers, source.pkgdir, source.resource)
-    end
-
-    if data.respond_to? :persistence_path
-      data.read
-      data
-    else
-      h = data.dup
-      data.clear
-      data.annotate h
-    end
-  end
-
-  def self.parse_header(stream, options = {})
-    case
-    when Path === stream 
-      stream.open do |f|
-        f.no_fail = true if ConcurrentStream === f
-        Parser.new f, options
-      end
-    when (String === stream and stream.length < 300 and (Open.exists? stream or Open.remote? stream))
-      Open.open(stream) do |f|
-        f.no_fail = true if ConcurrentStream === f
-        Parser.new f, options
-      end
-    else
-      filename = stream.respond_to?(:filename) ? stream.filename : Misc.fingerprint(stream)
-      Log.debug("Parsing header of open stream: #{filename}")
-      Parser.new stream, options
-    end
-  end
-
-  def self.parse(stream, data, options = {})
-
-    parser = Misc.process_options options, :parser
-    parser = TSV::Parser.new stream, options if parser.nil?
-
-    # dump with tchmgr
-    if defined? TokyoCabinet and TokyoCabinet::HDB === data and parser.straight and
-      data.close
-      begin
-        bin = 'tchmgr'
-        CMD.cmd("#{bin} version", :log => false)
-        FileUtils.mkdir_p File.dirname(data.persistence_path)
-        CMD.cmd("#{bin} importtsv '#{data.persistence_path}'", :in => stream, :log => false, :dont_close_in => true)
-      rescue
-        Log.debug("tchmgr importtsv failed for: #{data.persistence_path}")
-      end
-      data.write
-    end
-
-    # make TSV
-    data.extend TSV unless TSV === data
-    data.unnamed = true
-
-    # choose serializer
-    if data.serializer == :type
-      data.serializer = case
-                        when parser.cast.nil?
-                          data.serializer = parser.type
-                        when (parser.cast == :to_i and (parser.type == :list or parser.type == :flat))
-                          data.serializer = :integer_array
-                        when (parser.cast == :to_i and parser.type == :single)
-                          data.serializer = :integer
-                        when (parser.cast == :to_f and parser.type == :single)
-                          data.serializer = :float
-                        when (parser.cast == :to_f and (parser.type == :list or parser.type == :flat))
-                          data.serializer = :float_array
-                        else
-                          data.serializer = :marshal
-                        end
-    end
-
-    parser.traverse(options) do |key,values|
-      parser.add_to_data data, key, values
-    end
-
-    # setup the TSV
-    parser.setup data
-
-    data.unnamed = false
-
-    data
-  end
-end
+require_relative 'refactor'
+Rbbt.require_instead 'scout/tsv'
+require_relative 'tsv/refactor'
+#require 'rbbt/persist'
+#require 'rbbt/persist/tsv'
+#
+#require 'rbbt/util/log'
+#require 'rbbt/util/misc'
+#require 'rbbt/util/named_array'
+#
+#require 'rbbt/tsv/util'
+#require 'rbbt/tsv/serializers'
+#require 'rbbt/tsv/parser'
+#require 'rbbt/tsv/accessor'
+#require 'rbbt/tsv/manipulate'
+#require 'rbbt/tsv/index'
+#require 'rbbt/tsv/attach'
+#require 'rbbt/tsv/filter'
+#require 'rbbt/tsv/field_index'
+#require 'rbbt/tsv/parallel'
+#require 'rbbt/tsv/stream'
+#require 'rbbt/tsv/melt'
+#require 'rbbt/tsv/matrix'
+#require 'rbbt/tsv/marshal'
+#
+#module TSV
+#  class << self
+#    attr_accessor :lock_dir, :unnamed
+#    
+#    def lock_dir
+#      @lock_dir ||= Rbbt.tmp.tsv_open_locks.find
+#    end
+#  end
+#
+#  def self.str2options(str)
+#    field_options,_sep, rest =  str.partition("#")
+#    key, fields_str = field_options.split("~")
+#
+#    fields = fields_str.nil? ? [] : fields_str.split(/,\s*/)
+#
+#    rest = ":type=" << rest if rest =~ /^:?\w+$/
+#    rest_options = rest.nil? ? {} : Misc.string2hash(rest)
+#
+#    {:key_field => key, :fields => fields}.merge(rest_options)
+#  end
+#
+#  def self.setup(hash, type = nil, options = nil)
+#    type, options = nil, type if options.nil? and (Hash === type or (String === type and type.include? "~"))
+#    options = TSV.str2options(options) if String === options and options.include? "~"
+#    options ||= {}
+#    options[:type] ||= type unless type.nil?
+#
+#    options = Misc.add_defaults options, :default_value => [], :unnamed => TSV.unnamed
+#    default_value = Misc.process_options options, :default_value
+#    hash = Misc.array2hash(hash, default_value) if Array === hash
+#    hash.extend TSV
+#
+#    IndiferentHash.setup(options)
+#    ENTRIES.each do |entry|
+#      hash.send("#{ entry }=", options[entry.to_s]) if options.include? entry.to_s
+#      hash.send("#{ entry }=", options[entry.to_sym]) if options.include? entry.to_sym
+#    end
+#
+#    hash.unnamed = options[:unnamed]
+#
+#    hash
+#  end
+#
+#  # options shift if type.nil?
+#  def self.open(source, type = nil, options = nil)
+#    type, options = nil, type if options.nil? and (Hash === type or (String === type and type.include? "~"))
+#    options = TSV.str2options(options) if String === options and options.include? "~"
+#    options ||= {}
+#    options[:type] ||= type unless type.nil?
+#
+#    persist_options = Misc.pull_keys options, :persist
+#
+#    raise "TSV source is nil" if source.nil?
+#
+#    filename = get_filename source
+#    serializer = Misc.process_options options, :serializer
+#    unnamed = Misc.process_options options, :unnamed
+#    entity_options = Misc.process_options options, :entity_options
+#
+#
+#    Log.debug "TSV open: #{ filename } - #{Misc.fingerprint options }.#{unnamed ? " [unnamed]" : "[not unnamed]"}"
+#
+#    data = nil
+#
+#    lock_filename = filename.nil? ? nil : Persist.persistence_path(filename + '.open', {:dir => TSV.lock_dir})
+#    Misc.lock lock_filename  do
+#      data = Persist.persist_tsv source, filename, options, persist_options do |data|
+#        if serializer
+#          data.extend TSV unless TSV === data
+#          data.serializer = serializer
+#        end
+#
+#        tsv_grep = Misc.process_options options, :tsv_grep
+#        tsv_grep ||= Misc.process_options options, :grep
+#        open_options = Misc.pull_keys options, :open
+#
+#        stream = get_stream source, options.merge(open_options)
+#        parse stream, data, options.merge(:tsv_grep => tsv_grep)
+#
+#        if ! open_options[:noclose]
+#          stream.close unless stream.closed?
+#          stream.join if stream.respond_to?(:join)
+#        end
+#
+#        data.filename = filename.to_s unless filename.nil?
+#
+#        if data.identifiers.nil? and Path === filename and filename.identifier_file_path
+#          data.identifiers = filename.identifier_file_path.find if filename.identifier_file_path.exists?
+#        end
+#
+#        data
+#      end
+#    end
+#
+#
+#    data.unnamed = unnamed unless unnamed.nil?
+#
+#    data.entity_options = entity_options
+#
+#    if Path === source && data.identifiers
+#      Path.setup(data.identifiers, source.pkgdir, source.resource)
+#    end
+#
+#    if data.respond_to? :persistence_path
+#      data.read
+#      data
+#    else
+#      h = data.dup
+#      data.clear
+#      data.annotate h
+#    end
+#  end
+#
+#  def self.parse_header(stream, options = {})
+#    case
+#    when Path === stream 
+#      stream.open do |f|
+#        f.no_fail = true if ConcurrentStream === f
+#        Parser.new f, options
+#      end
+#    when (String === stream and stream.length < 300 and (Open.exists? stream or Open.remote? stream))
+#      Open.open(stream) do |f|
+#        f.no_fail = true if ConcurrentStream === f
+#        Parser.new f, options
+#      end
+#    else
+#      filename = stream.respond_to?(:filename) ? stream.filename : Misc.fingerprint(stream)
+#      Log.debug("Parsing header of open stream: #{filename}")
+#      Parser.new stream, options
+#    end
+#  end
+#
+#  def self.parse(stream, data, options = {})
+#
+#    parser = Misc.process_options options, :parser
+#    parser = TSV::Parser.new stream, options if parser.nil?
+#
+#    # dump with tchmgr
+#    if defined? TokyoCabinet and TokyoCabinet::HDB === data and parser.straight and
+#      data.close
+#      begin
+#        bin = 'tchmgr'
+#        CMD.cmd("#{bin} version", :log => false)
+#        FileUtils.mkdir_p File.dirname(data.persistence_path)
+#        CMD.cmd("#{bin} importtsv '#{data.persistence_path}'", :in => stream, :log => false, :dont_close_in => true)
+#      rescue
+#        Log.debug("tchmgr importtsv failed for: #{data.persistence_path}")
+#      end
+#      data.write
+#    end
+#
+#    # make TSV
+#    data.extend TSV unless TSV === data
+#    data.unnamed = true
+#
+#    # choose serializer
+#    if data.serializer == :type
+#      data.serializer = case
+#                        when parser.cast.nil?
+#                          data.serializer = parser.type
+#                        when (parser.cast == :to_i and (parser.type == :list or parser.type == :flat))
+#                          data.serializer = :integer_array
+#                        when (parser.cast == :to_i and parser.type == :single)
+#                          data.serializer = :integer
+#                        when (parser.cast == :to_f and parser.type == :single)
+#                          data.serializer = :float
+#                        when (parser.cast == :to_f and (parser.type == :list or parser.type == :flat))
+#                          data.serializer = :float_array
+#                        else
+#                          data.serializer = :marshal
+#                        end
+#    end
+#
+#    parser.traverse(options) do |key,values|
+#      parser.add_to_data data, key, values
+#    end
+#
+#    # setup the TSV
+#    parser.setup data
+#
+#    data.unnamed = false
+#
+#    data
+#  end
+#end

data/lib/rbbt/util/R/eval.rb

@@ -27,7 +27,7 @@ module R
       @@semfile 
     else
       @@semfile = File.basename(socket_file) + '.sem'
-      RbbtSemaphore.create_semaphore(@@semfile,1) 
+      ScoutSemaphore.create_semaphore(@@semfile,1) 
       @@semfile
     end
   end
@@ -42,7 +42,7 @@ module R
 
   def self.clear
     @@instance = nil
-    if defined? @@instance_process and @@instance_process and Misc.pid_exists? @@instance_process
+    if defined? @@instance_process and @@instance_process and Misc.pid_alive? @@instance_process
       Log.warn "Clearing Rserver session #{SESSION}, PID #{@@instance_process}"
       begin
         Process.kill :INT, @@instance_process
@@ -59,7 +59,7 @@ module R
   def self.instance
     @@instance ||= begin
 
-                     clear if File.exist? pid_file and ! Misc.pid_exists?(Open.read(pid_file).strip.to_i)
+                     clear if File.exist? pid_file and ! Misc.pid_alive?(Open.read(pid_file).strip.to_i)
 
                      FileUtils.mkdir_p File.dirname(socket_file) unless File.directory?(File.dirname(socket_file))
                      FileUtils.mkdir_p workdir unless File.directory? workdir
@@ -120,7 +120,7 @@ module R
   end
 
   def self._eval(cmd)
-    RbbtSemaphore.synchronize(semfile) do 
+    ScoutSemaphore.synchronize(semfile) do 
       times = 1
       begin
         instance.eval(cmd)