Module: Persist

Defined in:
lib/rbbt/persist.rb,
lib/rbbt/persist/tsv.rb

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"]
TC_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

Class Method Details

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

Returns:

  • (Boolean) 


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

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
      return false if check.select{|file| newer? path, file}.any?
   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 79

def self.load_file(path, type)
  case (type || "nil").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
    Marshal.load(Open.open(path))
  when :yaml
    YAML.load(Open.open(path))
  when :float
    Open.read(path).to_f
  when :integer
    Open.read(path).to_i
  else
    raise "Unknown persistence: #{ type }"
  end
end

.newer?(path, file) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/persist.rb', line 22

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



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

def self.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB)
  write = true if not File.exists?(path)

  tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB"
  tokyocabinet_class = TokyoCabinet::BDB if tokyocabinet_class == "BDB"

  flags = (write ? tokyocabinet_class::OWRITER | tokyocabinet_class::OCREAT : tokyocabinet_class::OREADER)

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

  database = TC_CONNECTIONS[path] ||= tokyocabinet_class.new
  database.close

  if !database.open(path, flags)
    ecode = database.ecode
    raise "Open error: #{database.errmsg(ecode)}. Trying to open file #{path}"
  end

  if not database.respond_to? :old_close
    class << database
      attr_accessor :writable, :closed, :persistence_path, :tokyocabinet_class

      def prefix(key)
        range(key, 1, key + 255.chr, 1)
      end

      def closed?
        @closed
      end

      alias old_close close
      def close
        @closed = true
        old_close
      end

      def read(force = false)
        return if not write? and not closed and not force
        self.close
        if !self.open(@persistence_path, tokyocabinet_class::OREADER)
          ecode = self.ecode
          raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
        end
        @writable = false
        @closed = false
        self
      end

      def write(force = true)
        return if write? and not closed and not force
        self.close

        if !self.open(@persistence_path, tokyocabinet_class::OWRITER)
          ecode = self.ecode
          raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
        end

        @writable = true
        @closed = false
        self
      end

      def write?
        @writable
      end

      def collect
        res = []
        each do |key, value|
          res << if block_given?
                   yield key, value
          else
            [key, value]
          end
        end
        res
      end

      def delete(key)
        out(key)
      end

      def write_and_read
        lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
        Misc.lock(lock_filename) do
          write if @closed or not write?
          res = begin
                  yield
                ensure
                  read
                end
          res
        end
      end


      def write_and_close
        lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
        Misc.lock(lock_filename) do
          write if @closed or not write?
          res = begin
                  yield
                ensure
                  close
                end
          res
        end
      end

      def read_and_close
        read if @closed or write?
        res = begin
                yield
              ensure
                close
              end
        res
      end

      def merge!(hash)
        hash.each do |key,values|
          self[key] = values
        end
      end

      if instance_methods.include? "range"
        alias old_range range

        def range(*args)
          keys = old_range(*args)
          keys - TSV::ENTRY_KEYS
        end
      end
    end
  end

  database.persistence_path ||= path
  database.tokyocabinet_class = tokyocabinet_class

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

  database
end

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



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# File 'lib/rbbt/persist.rb', line 161

def self.persist(name, type = nil, persist_options = {})
  type ||= :marshal
  persist_options = Misc.add_defaults persist_options, :persist => true
  other_options = Misc.process_options persist_options, :other

  if persist_options[:persist]
    path = persistence_path(name, persist_options, other_options || {})

    case 
    when type.to_sym === :memory
      Persist::MEMORY[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

      if is_persisted?(path, persist_options)
        Log.low "Persist up-to-date: #{ path } - #{persist_options.inspect[0..100]}"
        return nil if persist_options[:no_load]
        return load_file(path, type) 
      else
        Log.medium "Persist create: #{ path } - #{persist_options.inspect[0..100]}"
      end

      begin
        res = yield
        Misc.lock(path) do
          save_file(path, type, res)
        end
        res
      rescue
        Log.high "Error in persist. #{Open.exists?(path) ? "Erasing '#{ path }'" : ""}"
        FileUtils.rm path if Open.exists? path 
        raise $!
      end
    end

  else
    yield
  end
end

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



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# File 'lib/rbbt/persist/tsv.rb', line 158

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

  data = case
         when persist_options[:data]
           persist_options[:data]
         when persist_options[:persist]

           filename ||= 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)}]"
                        else
                          source.object_id.to_s
                        end

           filename ||= source.object_id.to_s

           path = persistence_path(filename, persist_options, options)

           if is_persisted? path and not persist_options[:update]
             Log.debug "TSV persistence up-to-date: #{ path }"
             lock_filename = Persist.persistence_path(path, {:dir => Rbbt.tmp.tsv_open_locks.find})
             return Misc.lock(lock_filename) do open_tokyocabinet(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB); end
           else
             Log.medium "TSV persistence creating: #{ path }"
           end

           FileUtils.rm path if File.exists? path

           data = open_tokyocabinet(path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB)
           data.serializer = :type if TSV === data and data.serializer.nil?

           data.close

           data
         else
           {}
         end

  begin
    if data.respond_to? :persistence_path and data != persist_options[:data]
      data.write_and_close do
        yield data
      end
    else
      yield data
    end
  rescue Exception
    FileUtils.rm path if path and File.exists? path
    raise $!
  ensure
    begin
      data.close if data.respond_to? :close
    rescue
      raise $!
    end
  end

  data.read if data.respond_to? :read and ((data.respond_to?(:write?) and data.write?) or (data.respond_to?(:closed?) and data.closed?))


  data
end

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



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# File 'lib/rbbt/persist.rb', line 44

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.gsub(/\//, '>') 
  else
    perfile = prefix.to_s + ":" + file.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) ⇒ Object 



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# File 'lib/rbbt/persist.rb', line 118

def self.save_file(path, type, content)

  return if content.nil?
  
  case (type || "nil").to_sym
  when :nil
    nil
  when :boolean
    Open.write(path, content ? "true" : "false")
  when :fwt
    content.file.seek 0
    Open.write(path, content.file.read)
  when :tsv
    Open.write(path, content.to_s)
  when :annotations
    Open.write(path, Annotated.tsv(content, :all).to_s)
  when :string, :text
    Open.write(path, content)
  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
    if content.empty?
      Open.write(path, "")
    else
      Open.write(path, content * "\n" + "\n")
    end
  when :marshal_tsv
    Open.write(path, Marshal.dump(content.dup))
  when :marshal
    Open.write(path, Marshal.dump(content))
  when :yaml
    Open.write(path, YAML.dump(content))
  when :float, :integer, :tsv
    Open.write(path, content.to_s)
  else
    raise "Unknown persistence: #{ type }"
  end
end