Summary

Bio::Root::Storable - object serialisation methods

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  my $storable = Bio::Root::Storable->new();

  # Store/retrieve using class retriever
  my $token     = $storable->store();
  my $storable2 = Bio::Root::Storable->retrieve( $token );

  # Store/retrieve using object retriever
  my $storable2 = $storable->new_retrievable();
  $storable2->retrieve();

Description

Generic module that allows objects to be safely stored/retrieved from
disk. Can be inhereted by any BioPerl object. As it will not usually
be the first class in the inheretence list, _initialise_storable()
should be called during object instantiation.
Object storage is recursive; If the object being stored contains other
storable objects, these will be stored seperately, and replaced by a
skeleton object in the parent heirarchy. When the parent is later
retrieved, its children remain in the skeleton state until explicitly
retrieved by the parent. This lazy-retrieve approach has obvious
memory efficiency benefits for certain applications.
By default, objects are stored in binary format (using the Perl
Storable module). Earlier versions of Perl5 do not include Storable as
a core module. If this is the case, ASCII object storage (using the
Perl Data::Dumper module) is used instead.
ASCII storage can be enabled by default by setting the value of
$Bio::Root::Storable::BINARY to false.

Methods

Methods description

  Arg [1]   : -workdir  => filesystem path,
              -template => tmpfile template,
              -suffix   => tmpfile suffix,
  Function  : Builds a new Bio::Root::Storable inhereting object
  Returntype: Bio::Root::Storable inhereting object
  Exceptions: 
  Caller    : 
  Example   : $storable = Bio::Root::Storable->new()

  Arg [1]   : See 'new' method
  Function  : Initialises storable-specific attributes
  Returntype: boolean
  Exceptions: 
  Caller    : 
  Example   :

  Arg [1]   : string (optional)
  Function  : Accessor for the file to write state into.
              Should not normaly use as a setter - let Root::IO
              do this for you.
  Returntype: string
  Exceptions: 
  Caller    : Bio::Root::Storable->store
  Example   : my $statefile = $obj->statefile();

  Arg [1]   : string (optional) (TODO - convert to array for x-platform)
  Function  : Accessor for the statefile directory. Defaults to
              $Bio::Root::IO::TEMPDIR
  Returntype: string
  Exceptions: 
  Caller    : 
  Example   : $obj->workdir('/tmp/foo');

  Arg [1]   : string (optional)
  Function  : Accessor for the statefile template. Defaults to XXXXXXXX
  Returntype: string
  Exceptions: 
  Caller    : 
  Example   : $obj->workdir('RES_XXXXXXXX');

  Arg [1]   : string (optional)
  Function  : Accessor for the statefile template.
  Returntype: string
  Exceptions: 
  Caller    : 
  Example   : $obj->suffix('.state');

  Arg [1]   : Same as for 'new'
  Function  : Similar to store, except returns a 'skeleton' of the calling
              object, rather than the statefile.
              The skeleton can be repopulated by calling 'retrieve'. This
              will be a clone of the original object.
  Returntype: Bio::Root::Storable inhereting object
  Exceptions: 
  Caller    : 
  Example   : my $skel = $obj->new_retrievable(); # skeleton 
              $skel->retrieve();                  # clone

  Arg [1]   : none
  Function  : Reports whether the object is in 'skeleton' state, and the
              'retrieve' method can be called.
  Returntype: boolean
  Exceptions: 
  Caller    : 
  Example   : if( $obj->retrievable ){ $obj->retrieve }

  Arg [1]   : None
  Function  : Accessor for token attribute
  Returntype: string. Whatever retrieve needs to retrieve.
              This base implementation returns the statefile
  Exceptions: 
  Caller    : 
  Example   : my $token = $obj->token();

  Arg [1]   : none
  Function  : Saves a serialised representation of the object structure
              to disk. Returns the name of the file that the object was
              saved to.
  Returntype: string

  Exceptions: 
  Caller    : 
  Example   : my $token = $obj->store();

  Arg [1]   : none
  Function  : Prepares the the serialised representation of the object.
              Object attribute names starting with '__' are skipped.
              This is useful for those that do not serialise too well
              (e.g. filehandles).
              Attributes are examined for other storable objects. If these
              are found they are serialised seperately using 'new_retrievable'
  Returntype: string
  Exceptions: 
  Caller    : 
  Example   : my $serialised = $obj->serialise();

  Arg [1]   : string; filesystem location of the state file to be retrieved
  Function  : Retrieves a stored object from disk.
              Note that the retrieved object will be blessed into its original
              class, and not the
  Returntype: Bio::Root::Storable inhereting object
  Exceptions: 
  Caller    : 
  Example   : my $obj = Bio::Root::Storable->retrieve( $token );

  Arg [1]   : none
  Function  : Returns a clone of the calling object
  Returntype: Bio::Root::Storable inhereting object
  Exceptions: 
  Caller    : 
  Example   : my $clone = $obj->clone();

  Arg [1]   : none
  Function  : Clears the stored object from disk
  Returntype: boolean
  Exceptions: 
  Caller    : 
  Example   : $obj->remove();

  Arg [1]   : variable
  Function  : Converts whatever is in the the arg into a string.
              Uses either Storable::freeze or Data::Dumper::Dump
              depending on the value of $Bio::Root::BINARY
  Returntype: 
  Exceptions: 
  Caller    : 
  Example   :

  Arg [1]   : string
  Function  : Converts the string into a perl 'whatever'.
              Uses either Storable::thaw or eval depending on the
              value of $Bio::Root::BINARY.
              Note; the string arg should have been created with 
              the _freeze method, or strange things may occur!
  Returntype: variable
  Exceptions: 
  Caller    : 
  Example   :

Methods code

BEGIN {

  if( eval "require Storable" ){
    Storable->import( 'freeze', 'thaw' );
    $BINARY = 1;

}

sub new {

  my ($caller, @args) = @_;
  my $self = $caller->SUPER::new(@args);
  $self->_initialise_storable;
  return $self;

}

sub _initialise_storable {

  my $self = shift;
  my( $workdir, $template, $suffix ) =
    $self->_rearrange([qw(WORKDIR TEMPLATE SUFFIX)], @_ );
  $workdir  && $self->workdir ( $workdir );
  $template && $self->template( $template );
  $suffix   && $self->suffix  ( $suffix   );
  return 1;

}

sub statefile {

  my $key = '_statefile';
  my $self  = shift;

  if( @_ ){ $self->{$key} = shift }

  if( ! $self->{$key} ){ # Create a new statefile

    my $workdir  = $self->workdir;
    my $template = $self->template;
    my $suffix   = $self->suffix;

    # TODO: add cleanup and unlink methods. For now, we'll keep the
    # statefile hanging around.
    my @args = ( CLEANUP=>0, UNLINK=>0 );
    if( $template ){ push( @args, 'TEMPLATE' => $template )};
    if( $workdir  ){ push( @args, 'DIR'      => $workdir  )};
    if( $suffix   ){ push( @args, 'SUFFIX'   => $suffix   )};
    my( $fh, $file ) = Bio::Root::IO->new->tempfile( @args );

    $self->{$key} = $file;
  }

  return $self->{$key};

}

sub workdir {

  my $key = '_workdir';
  my $self = shift;
  if( @_ ){
    my $caller = join( ', ', (caller(0))[1..2] );
    $self->{$key} && $self->debug("Overwriting workdir: probably bad!");
    $self->{$key} = shift
  }
  $self->{$key} ||= $Bio::Root::IO::TEMPDIR;
  return $self->{$key};

}

sub template {

  my $key = '_template';
  my $self = shift;
  if( @_ ){ $self->{$key} = shift }
  $self->{$key} ||= 'XXXXXXXX';
  return $self->{$key};

}

sub suffix {

  my $key = '_suffix';
  my $self = shift;
  if( @_ ){ $self->{$key} = shift }
  return $self->{$key};

}

sub new_retrievable {

   my $self = shift;
   my @args = @_;

   $self->_initialise_storable( @args );

   if( $self->retrievable ){ return $self->clone } # Clone retrievable
   return bless( { _statefile   => $self->store(@args),
		   _workdir     => $self->workdir,
		   _suffix      => $self->suffix,
		   _template    => $self->template,
		   _retrievable => 1 }, ref( $self ) );

}

sub retrievable {

   my $self = shift;
   if( @_ ){ $self->{_retrievable} = shift }
   return $self->{_retrievable};

}

sub token {

  my $self = shift;
  return $self->statefile;

}

sub store {

  my $self = shift;
  my $statefile = $self->statefile;
  my $store_obj = $self->serialise;
  my $io = Bio::Root::IO->new( ">$statefile" );
  $io->_print( $self->_freeze( $store_obj ) );
  $self->debug( "STORING $store_obj to $statefile\n" );
  return $statefile;

}

sub serialise {

  my $self = shift;

  # Create a new object of same class that is going to be serialised
  my $store_obj = bless( {}, ref( $self ) );

  my %retargs = ( -workdir =>$self->workdir,
		  -suffix  =>$self->suffix,
		  -template=>$self->template );
  # Assume that other storable bio objects held by this object are
  # only 1-deep.

  foreach my $key( keys( %$self ) ){
    if( $key =~ /^__/ ){ next } # Ignore keys starting with '__'
    my $value = $self->{$key};

    # Scalar value
    if( ! ref( $value ) ){
      $store_obj->{$key} = $value;
    }

    # Bio::Root::Storable obj: save placeholder
    elsif( ref($value) =~ /^Bio::/ and $value->isa('Bio::Root::Storable') ){
      # Bio::Root::Storable
      $store_obj->{$key} = $value->new_retrievable( %retargs );
      next;
    }

    # Arrayref value. Look for Bio::Root::Storable objs
    elsif( ref( $value ) eq 'ARRAY' ){
      my @ary;
      foreach my $val( @$value ){
	if( ref($val) =~ /^Bio::/ and $val->isa('Bio::Root::Storable') ){
	  push(  @ary, $val->new_retrievable( %retargs ) );
	}
	else{ push(  @ary, $val ) }
      }
      $store_obj->{$key} =\@ ary;
    }

    # Hashref value. Look for Bio::Root::Storable objs
    elsif( ref( $value ) eq 'HASH' ){
      my %hash;
      foreach my $k2( keys %$value ){
	my $val = $value->{$k2};
	if( ref($val) =~ /^Bio::/ and $val->isa('Bio::Root::Storable') ){
	  $hash{$k2} = $val->new_retrievable( %retargs );
	}
	else{ $hash{$k2} = $val }
      }
      $store_obj->{$key} =\% hash;
    }

    # Unknown, just add to the store object regardless
    else{ $store_obj->{$key} = $value }
  }
  $store_obj->retrievable(0); # Once deserialised, obj not retrievable
  return $store_obj;

}

sub retrieve {

  my( $caller, $statefile ) = @_;

  my $self = {};
  my $class = ref( $caller ) || $caller;

  # Is this a call on a retrievable object?
  if( ref( $caller ) and
      $caller->retrievable ){
    $self = $caller;
    $statefile = $self->statefile;
  }
  bless( $self, $class );

  # Recover serialised object
  if( ! -f $statefile ){
    $self->throw( "Token $statefile is not found" );
  }
  my $io = Bio::Root::IO->new( $statefile );
  local $/ = undef();
  my $state_str = $io->_readline;

  # Dynamic-load modules required by stored object
  my $stored_obj;
  my $success;
  for( my $i=0; $i<10; $i++ ){
    eval{ $stored_obj = $self->_thaw( $state_str ) };
    if( ! $@ ){ $success=1; last }
    my $package;
    if( $@ =~ /Cannot restore overloading/i ){
      my $postmatch = $';
      if( $postmatch =~ /\(package +([\w\:]+)\)/ ) {
	$package = $1;
      }
    }
    if( $package ){
      eval "require $package"; $self->throw($@) if $@;
    }
    else{ $self->throw($@) }
  }
  if( ! $success ){ $self->throw("maximum number of requires exceeded" ) }

  if( ! ref( $stored_obj ) ){
    $self->throw( "Token $statefile returned no data" );
  }
  map{ $self->{$_} = $stored_obj->{$_} } keys %$stored_obj; # Copy hasheys
  $self->retrievable(0);

  # Maintain class of stored obj
  return $self;

}

sub clone {

  my $self = shift;
  my $frozen = $self->_freeze( $self );
  return $self->_thaw( $frozen );

}

sub remove {

  my $self = shift;
  if( -e $self->statefile ){
    unlink( $self->statefile );
  }
  return 1;

}

sub _freeze {

  my $self = shift;
  my $data = shift;
  if( $BINARY ){
    return freeze( $data );
  }
  else{
    $Data::Dumper::Purity = 1;
    return Data::Dumper->Dump( [\$data],["*code"] );
  }

}

sub _thaw {

  my $self = shift;
  my $data = shift;
  if( $BINARY ){ return thaw( $data ) }
  else{ 
    my $code; 
    $code = eval( $data ) ;
    if($@) {
      die( "eval: $@" );
    }   
    ref( $code ) eq 'REF' || 
      $self->throw( "Serialised string was not a scalar ref" );
    return $$code;
  }

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bio.perl.org

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email whs@sanger.ac.uk

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _