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 separately, 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, object storage (using the Perl Data::Dumper module) is used instead.

storage can be enabled by default by setting the value of to false.

FEEDBACK

Mailing Lists

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.

 [email protected]

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

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

 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Will Spooner

Email [email protected]

APPENDIX

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

new

 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()

_initialise_storable

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

statefile

 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();

workdir

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

template

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

suffix

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

new_retrievable

 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

retrievable

 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 }

token

 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();

store

 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();

serialise

 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 separately using 'new_retrievable'
 Returntype: string
 Exceptions: 
 Caller : 
 Example : my $serialised = $obj->serialise();

retrieve

 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 );

clone

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

remove

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

_freeze

 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 :

_thaw

 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 :