Module: Persist

Defined in:
lib/rbbt/persist.rb,
lib/rbbt/persist/tsv.rb,
lib/rbbt/persist/tsv/cdb.rb,
lib/rbbt/persist/tsv/lmdb.rb,
lib/rbbt/persist/tsv/adapter.rb,
lib/rbbt/persist/tsv/leveldb.rb,
lib/rbbt/persist/tsv/sharder.rb,
lib/rbbt/persist/tsv/kyotocabinet.rb,
lib/rbbt/persist/tsv/packed_index.rb,
lib/rbbt/persist/tsv/tokyocabinet.rb,
lib/rbbt/persist/tsv/fix_width_table.rb

Defined Under Namespace

Modules: CDBAdapter, FWTAdapter, KCAdapter, LMDBAdapter, LevelDBAdapter, PKIAdapter, SharderAdapter, TCAdapter, TSVAdapter Classes: Sharder

Constant Summary collapse

MEMORY = 
{}
MAX_FILE_LENGTH = 
150
TRUE_STRINGS = 
Set.new ["true", "True", "TRUE", "t", "T", "1", "yes", "Yes", "YES", "y", "Y", "ON", "on"]
CONNECTIONS = 
{}

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.cachedir ⇒ Object

Returns the value of attribute cachedir.



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# File 'lib/rbbt/persist.rb', line 10

def cachedir
  @cachedir
end

.lock_dir ⇒ Object

Returns the value of attribute lock_dir.



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# File 'lib/rbbt/persist.rb', line 18

def lock_dir
  @lock_dir
end

Class Method Details

.get_filename(source) ⇒ Object 



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# File 'lib/rbbt/persist/tsv.rb', line 39

def self.get_filename(source)
  case
  when Path === source
    source
  when (source.respond_to?(:filename) and source.filename)
    source.filename
  when source.respond_to?(:cmd)
    "CMD-#{Misc.digest(source.cmd)}"
  when TSV === source
    "TSV[#{Misc.digest Misc.fingerprint(source)}]"
  end || source.object_id.to_s
end

.get_result(path, type, persist_options, lockfile, &block) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 220

def self.get_result(path, type, persist_options, lockfile, &block)
  res = yield path
  stream = res if IO === res
  stream = res.stream if res.respond_to? :stream

  if stream
    if persist_options[:no_load] == :stream 
      res = tee_stream(stream, path, type, stream.respond_to?(:callback)? stream.callback : nil, stream.respond_to?(:abort_callback)? stream.abort_callback : nil, lockfile)
      #res.lockfile = lockfile

      raise KeepLocked.new res 
    else
      stream = res.get_stream if res.respond_to? :get_stream
      begin
        Open.write(path, stream)
        Open.open(path) do |stream|
          case type
          when :array
            stream.read.split "\n"
          when :tsv
            TSV.open(stream)
          else
            stream.read
          end
        end
      rescue
        stream.abort if stream.respond_to? :abort
        raise $!
      end
    end
  else
    res
  end
end

.is_persisted?(path, persist_options = {}) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/persist.rb', line 34

def self.is_persisted?(path, persist_options = {})
  return false if not Open.exists? path
  return false if TrueClass === persist_options[:update]

  check = persist_options[:check]
  if not check.nil?
    if Array === check
      if check.select{|file| newer? path, file}.any?
        Log.medium "Persistence check for #{path} failed in: #{ check.select{|file| newer? path, file} * ", "}"
        return false 
      end
   else
      return false if newer? path, check
   end
  end

  return true
end

.load_file(path, type) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 88

def self.load_file(path, type)
  begin
    case (type || :marshal).to_sym
    when :nil
      nil
    when :boolean
      TRUE_STRINGS.include? Open.read(path).chomp.strip
    when :annotations
      Annotated.load_tsv TSV.open(path)
    when :tsv
      TSV.open(path)
    when :marshal_tsv
      TSV.setup(Marshal.load(Open.open(path)))
    when :fwt
      FixWidthTable.get(path) 
    when :string, :text
      Open.read(path)
    when :binary
      f = File.open(path, 'rb')
      res = f.read
      f.close
      res.force_encoding("ASCII-8BIT") if res.respond_to? :force_encoding
      res
    when :array
      res = Open.read(path).split("\n", -1)
      res.pop
      res
    when :marshal
      Open.open(path) do |stream|
        content = stream.read.unpack("m").first
        Marshal.load(content) 
      end
    when :yaml
      Open.open(path) do |stream|
        YAML.load(stream)
      end
    when :float
      Open.read(path).to_f
    when :integer
      Open.read(path).to_i
    else
      raise "Unknown persistence: #{ type }"
    end
  rescue
    Log.medium "Exception loading #{ type } #{ path }: #{$!.message}"
    raise $!
  end
end

.memory(name, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 416

def self.memory(name, options = {}, &block)
  case options
  when nil
    persist name, :memory, :file => name, &block
  when String
    persist name, :memory, :file => name + "_" << options, &block
  else
    file = name
    repo = options.delete :repo if options and options.any?
    file << "_" << (options[:key] ? options[:key] : Misc.hash2md5(options)) if options and options.any?
    persist name, :memory, {:repo => repo, :persist => true, :file => file}.merge(options), &block
  end
end

.newer?(path, file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/persist.rb', line 28

def self.newer?(path, file)
  return true if not Open.exists? file
  return true if File.mtime(path) < File.mtime(file)
  return false
end

.open_cdb(path, write, serializer = nil) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/cdb.rb', line 128

def self.open_cdb(path, write, serializer = nil)
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::CDBAdapter.open(path, write)

  #unless serializer == :clean
  #  TSV.setup database
  #  database.serializer = serializer if serializer
  #end

  database
end

.open_database(path, write, serializer = nil, type = "HDB", options = {}) ⇒ Object 



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# File 'lib/rbbt/persist/tsv.rb', line 52

def self.open_database(path, write, serializer = nil, type = "HDB", options = {})
  case type
  when "LevelDB"
    Persist.open_leveldb(path, write, serializer)
  when "CDB"
    Persist.open_cdb(path, write, serializer)
  when "LMDB"
    Persist.open_lmdb(path, write, serializer)
  when 'kch', 'kct'
    Persist.open_kyotocabinet(path, write, serializer, type)
  when 'fwt'
    value_size, range, update, in_memory, pos_function = Misc.process_options options.dup, :value_size, :range, :update, :in_memory, :pos_function
    if pos_function
      Persist.open_fwt(path, value_size, range, serializer, update, in_memory, &pos_function)
    else
      Persist.open_fwt(path, value_size, range, serializer, update, in_memory)
    end
  when 'pki'
    pattern, pos_function = Misc.process_options options.dup, :pattern, :pos_function
    if pos_function
      Persist.open_pki(path, write, pattern, &pos_function)
    else
      Persist.open_pki(path, write, pattern)
    end
  else
    Persist.open_tokyocabinet(path, write, serializer, type)
  end
end

.open_fwt(path, value_size, range = false, serializer = nil, update = false, in_memory = false, &pos_function) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/fix_width_table.rb', line 98

def self.open_fwt(path, value_size, range = false, serializer = nil, update = false, in_memory = false, &pos_function)
  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::FWTAdapter.open(path, value_size, range, update, in_memory, &pos_function)

  unless serializer == :clean
    TSV.setup database
    database.serializer = serializer || database.serializer
  end

  database
end

.open_kyotocabinet(path, write, serializer = nil, kyotocabinet_class = 'kch') ⇒ Object 



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# File 'lib/rbbt/persist/tsv/kyotocabinet.rb', line 80

def self.open_kyotocabinet(path, write, serializer = nil,  kyotocabinet_class= 'kch')
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::KCAdapter.open(path, write, kyotocabinet_class)

  unless serializer == :clean
    TSV.setup database
    database.serializer = serializer || database.serializer
  end

  database
end

.open_leveldb(path, write, serializer = nil) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/leveldb.rb', line 106

def self.open_leveldb(path, write, serializer = nil)
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::LevelDBAdapter.open(path, write)

  unless serializer == :clean
    TSV.setup database
    database.serializer = serializer || database.serializer
  end

  database
end

.open_lmdb(path, write, serializer = nil) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/lmdb.rb', line 47

def self.open_lmdb(path, write, serializer = nil)
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::LMDBAdapter.open(path, write)

  unless serializer == :clean
    TSV.setup database
    database.serializer = serializer || database.serializer
  end

  database
end

.open_pki(path, write, pattern, &pos_function) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/packed_index.rb', line 98

def self.open_pki(path, write, pattern, &pos_function)
  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::PKIAdapter.open(path, write, pattern, &pos_function)

  #TSV.setup database

  #database.serializer = :clean

  database
end

.open_sharder(path, write, serializer = nil, type = TokyoCabinet::HDB, options, &shard_function) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/sharder.rb', line 245

def self.open_sharder(path, write, serializer = nil, type = TokyoCabinet::HDB, options, &shard_function)
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::SharderAdapter.open(path, write, type, options, &shard_function)

  if type.to_s == 'pki'
    TSV.setup database
    database.type = :list
    database.serializer = :clean 
  else
    if serializer != :clean 
      TSV.setup database
      database.serializer = serializer if serializer
    end
  end

  database
end

.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB) ⇒ Object 



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# File 'lib/rbbt/persist/tsv/tokyocabinet.rb', line 189

def self.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB)
  write = true unless File.exists? path

  FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))

  database = Persist::TCAdapter.open(path, write, serializer, tokyocabinet_class)

  unless serializer == :clean
    TSV.setup database
    database.serializer = serializer || database.serializer
  end

  database
end

.persist(name, type = nil, persist_options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 311

def self.persist(name, type = nil, persist_options = {}, &block)
  type ||= :marshal

  persist_options ||= {}
  return (persist_options[:repo] || Persist::MEMORY)[persist_options[:file]] ||= yield if type ==:memory and persist_options[:file] and persist_options[:persist] and persist_options[:persist] != :update

  if FalseClass === persist_options[:persist]
    yield
  else
    persist_options[:update] ||= true if persist_options[:persist].to_s == "update"
    other_options = Misc.process_options persist_options, :other
    path = persistence_path(name, persist_options, other_options || {})

    case 
    when type.to_sym == :memory
      repo = persist_options[:repo] || Persist::MEMORY
      repo[path] ||= yield

    when (type.to_sym == :annotations and persist_options.include? :annotation_repo)

      repo = persist_options[:annotation_repo]

      keys = nil
      subkey = name + ":"

      if String === repo
        repo = Persist.open_tokyocabinet(repo, false, :list, "BDB")
        repo.read_and_close do
          keys = repo.range subkey + 0.chr, true, subkey + 254.chr, true
        end
        repo.close
      else
        repo.read_and_close do
          keys = repo.range subkey + 0.chr, true, subkey + 254.chr, true
        end
      end

      case
      when (keys.length == 1 and keys.first == subkey + 'NIL')
        nil
      when (keys.length == 1 and keys.first == subkey + 'EMPTY')
        []
      when (keys.length == 1 and keys.first =~ /:SINGLE$/)
        key = keys.first
        values = repo.read_and_close do
          repo[key]
        end
        Annotated.load_tsv_values(key, values, "literal", "annotation_types", "JSON")
      when (keys.any? and not keys.first =~ /ANNOTATED_DOUBLE_ARRAY/)
        repo.read_and_close do
          keys.sort_by{|k| k.split(":").last.to_i}.collect{|key|
            v = repo[key]
            Annotated.load_tsv_values(key, v, "literal", "annotation_types", "JSON")
          }
        end
      when (keys.any? and keys.first =~ /ANNOTATED_DOUBLE_ARRAY/)
        repo.read_and_close do

          res = keys.sort_by{|k| k.split(":").last.to_i}.collect{|key|
            v = repo[key]
            Annotated.load_tsv_values(key, v, "literal", "annotation_types", "JSON")
          }

          res.first.annotate res
          res.extend AnnotatedArray

          res
        end
      else
        entities = yield

        repo.write_and_close do 
          case
          when entities.nil?
            repo[subkey + "NIL"] = nil
          when entities.empty?
            repo[subkey + "EMPTY"] = nil
          when (not Array === entities or (AnnotatedArray === entities and not Array === entities.first))
            tsv_values = entities.tsv_values("literal", "annotation_types", "JSON") 
            repo[subkey + entities.id << ":" << "SINGLE"] = tsv_values
          when (not Array === entities or (AnnotatedArray === entities and AnnotatedArray === entities.first))
            entities.each_with_index do |e,i|
              next if e.nil?
              tsv_values = e.tsv_values("literal", "annotation_types", "JSON") 
              repo[subkey + e.id << ":ANNOTATED_DOUBLE_ARRAY:" << i.to_s] = tsv_values
            end
          else
            entities.each_with_index do |e,i|
              next if e.nil?
              tsv_values = e.tsv_values("literal", "annotation_types", "JSON") 
              repo[subkey + e.id << ":" << i.to_s] = tsv_values
            end
          end
        end

        entities
      end

    else
      persist_file(path, type, persist_options, &block)
    end

  end
end

.persist_file(path, type, persist_options, &block) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 255

def self.persist_file(path, type, persist_options, &block)
  begin
    if is_persisted?(path, persist_options)
      Log.low "Persist up-to-date: #{ path } - #{Misc.fingerprint persist_options}"
      return path if persist_options[:no_load]
      return load_file(path, type) 
    else
      Open.rm path if Open.exists? path
    end
  rescue Exception
    Open.rm path if Open.exists? path
  end

  lock_filename = Persist.persistence_path(path + '.persist', {:dir => Persist.lock_dir})
  begin
    lock_options = Misc.pull_keys persist_options, :lock
    lock_options = lock_options[:lock] if Hash === lock_options[:lock]
    Misc.lock lock_filename, lock_options do |lockfile|
      Misc.insist do
        if is_persisted?(path, persist_options)
          Log.low "Persist up-to-date (suddenly): #{ path } - #{Misc.fingerprint persist_options}"
          return path if persist_options[:no_load]
          return load_file(path, type) 
        end
      end

      Log.medium "Persist create: #{ path } - #{type} #{Misc.fingerprint persist_options}"

      res = get_result(path, type, persist_options, lockfile, &block)

      save_file(path, type, res, lockfile)

      return path if persist_options[:no_load]

      res
    end

  rescue Lockfile::StolenLockError
    begin
      Log.medium "Lockfile stolen: #{path}"
      sleep 1 + rand(2)
    rescue Exception
    end
    retry
  rescue Exception
    Log.medium "Error in persist: #{path}#{Open.exists?(path) ? Log.color(:red, " Erasing") : ""}"

    begin
      FileUtils.rm path 
    rescue
    end if Open.exists? path 

    raise $!
  end
end

.persist_tsv(source, filename, options = {}, persist_options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/persist/tsv.rb', line 81

def self.persist_tsv(source, filename, options = {}, persist_options = {}, &block)
  persist_options[:prefix] ||= "TSV"

  if data = persist_options[:data]
    yield data
    return data 
  end

  filename ||= get_filename(source)

  if not persist_options[:persist]
    data = {}

    yield(data) 

    return data 
  end

  path = persistence_path(filename, persist_options, options)

  lock_filename = Persist.persistence_path(path, {:dir => TSV.lock_dir})

  if is_persisted?(path) and not persist_options[:update]
    Log.debug "TSV persistence up-to-date: #{ path }"
    if persist_options[:shard_function]
      return open_sharder(path, false, nil, persist_options[:engine], persist_options, &persist_options[:shard_function]) 
    else
      return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB, persist_options) 
    end
  end

  Misc.lock lock_filename do
    begin
      if is_persisted?(path) and not persist_options[:update]
        Log.debug "TSV persistence (suddenly) up-to-date: #{ path }"

        if persist_options[:shard_function]
          return open_sharder(path, false, nil, persist_options[:engine], persist_options, &persist_options[:shard_function]) 
        else
          return open_database(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB, persist_options) 
        end
      end

      FileUtils.rm_rf path if File.exists? path

      Log.medium "TSV persistence creating: #{ path }"

      tmp_path = path + '.persist'

      data = if persist_options[:shard_function]
               open_sharder(tmp_path, true, persist_options[:serializer], persist_options[:engine], persist_options, &persist_options[:shard_function]) 
             else
               open_database(tmp_path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB, persist_options) 
             end

      if TSV === data and data.serializer.nil?
        data.serializer = :type 
      end

      data.write_and_read do
        yield data
      end

      FileUtils.mv data.persistence_path, path if File.exists? data.persistence_path and not File.exists? path
      tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
      tsv.persistence_path = path

      tsv.fix_io if tsv.respond_to? :fix_io

      data
    rescue Exception
      Log.error "Captured error during persist_tsv. Erasing: #{path}"
      FileUtils.rm_rf tmp_path if tmp_path and File.exists? tmp_path
      FileUtils.rm_rf path if path and File.exists? path
      raise $!
    end
  end
end

.persistence_path(file, persist_options = {}, options = {}) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 53

def self.persistence_path(file, persist_options = {}, options = {})
  persistence_file = Misc.process_options persist_options, :file
  return persistence_file unless persistence_file.nil?

  prefix = Misc.process_options persist_options, :prefix

  if prefix.nil?
    perfile = file.to_s.gsub(/\//, '>') 
  else
    perfile = prefix.to_s + ":" + file.to_s.gsub(/\//, '>') 
  end

  if options.include? :filters
    options[:filters].each do |match,value|
      perfile = perfile + "&F[#{match}=#{Misc.digest(value.inspect)}]"
    end
  end

  persistence_dir = Misc.process_options(persist_options, :dir) || Persist.cachedir 
  Path.setup(persistence_dir) unless Path === persistence_dir

  filename = perfile.gsub(/\s/,'_').gsub(/\//,'>')
  clean_options = options
  clean_options.delete :unnamed
  clean_options.delete "unnamed"

  filename = filename[0..MAX_FILE_LENGTH] << Misc.digest(filename[MAX_FILE_LENGTH+1..-1]) if filename.length > MAX_FILE_LENGTH + 10

  options_md5 = Misc.hash2md5 clean_options
  filename  << ":" << options_md5 unless options_md5.empty?

  persistence_dir[filename].find
end

.save_file(path, type, content, lockfile = nil) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 137

def self.save_file(path, type, content, lockfile = nil)
  if content.nil?
    lockfile.unlock if lockfile and lockfile.locked?
    return
  end

  case (type || :marshal).to_sym
  when :nil
    nil
  when :boolean
    Misc.sensiblewrite(path, content ? "true" : "false", :lock => lockfile)
  when :fwt
    content.file.seek 0
    Misc.sensiblewrite(path, content.file.read, :lock => lockfile)
  when :tsv
    content = content.to_s if TSV === content
    Misc.sensiblewrite(path, content, :lock => lockfile)
  when :annotations
    Misc.sensiblewrite(path, Annotated.tsv(content, :all).to_s, :lock => lockfile)
  when :string, :text
    Misc.sensiblewrite(path, content, :lock => lockfile)
  when :binary
    content.force_encoding("ASCII-8BIT") if content.respond_to? :force_encoding
    f = File.open(path, 'wb')
    f.puts content
    f.close
    content
  when :array
    case content
    when Array
      if content.empty?
        Misc.sensiblewrite(path, "", :lock => lockfile)
      else
        Misc.sensiblewrite(path, content * "\n" + "\n", :lock => lockfile)
      end
    when IO
      Misc.sensiblewrite(path, content, :lock => lockfile)
    else
      Misc.sensiblewrite(path, content.to_s, :lock => lockfile)
    end
  when :marshal_tsv
    Misc.sensiblewrite(path, Marshal.dump(content.dup), :lock => lockfile)
  when :marshal
    dump = Marshal.dump(content)
    Misc.sensiblewrite(path, [dump].pack("m"), :lock => lockfile)
  when :yaml
    Misc.sensiblewrite(path, YAML.dump(content), :lock => lockfile)
  when :float, :integer, :tsv
    Misc.sensiblewrite(path, content.to_s, :lock => lockfile)
  else
    raise "Unknown persistence: #{ type }"
  end
end

.tee_stream_thread(stream, path, type, callback = nil, abort_callback = nil, lockfile = nil) ⇒ Object Also known as: tee_stream 



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# File 'lib/rbbt/persist.rb', line 191

def self.tee_stream_thread(stream, path, type, callback = nil, abort_callback = nil, lockfile = nil)
  file, out = Misc.tee_stream(stream)

  saver_thread = Thread.new(Thread.current) do |parent|
    begin
      Thread.current["name"] = "file saver: " + path
      save_file(path, type, file, lockfile)
    rescue Aborted
      Log.medium "Persist stream thread aborted: #{ Log.color :blue, path }"
      file.abort if file.respond_to? :abort
      raise $!
    rescue Exception
      Log.medium "Persist stream thread exception: #{ Log.color :blue, path }"
      file.abort if file.respond_to? :abort
      parent.raise $!
      raise $!
    end
  end
  ConcurrentStream.setup(out, :threads => saver_thread, :filename => path)
  out.callback = callback
  out.abort_callback = abort_callback
  out.lockfile = stream.lockfile if stream.respond_to? :lockfile
  out
end