[Bioperl-l] Re: cloning and Storable

[Will Spooner]

On Fri, 5 Sep 2003, Heikki Lehvaslaiho wrote:

> Will,
> 
> This does not solve my problem but is a great module to add into
> bioperl. I'll do it right now if you promise to write a test file in
> near future. ;-)
> 
> 
> I added the following text into docs:
> 
> Anyone planning to use Bio::Root::Storable in bioperl modules:
> Storable is not part of all perl core libraries. When inheriting from
> it, you have to do:
>     eval { require Storable; };
> and fail gracefully.
> 

I have plans to add an ASCII option that replaces Storable with
Data::Dumper. That's a core Perl 5.8 module, but I don't know about
earlier versions.

Will


> 
> 	-Heikki
> 
> On Fri, 2003-09-05 at 09:39, Will Spooner wrote:
> > This may be a good time to mention that we have developed a
> > Bio::Root::Storable module for use with the Ensembl web site. 
> > 
> > This module is used specifically for serialising/retrieving Search objects
> > to disk after parsing with SearchIO. It is in production, and works very
> > well, even in a high-throughput environment.
> > 
> > The implementation is generic (can be inhereted by any bioperl object),
> > and even implements a clone() method.
> > 
> > I have attached the module to this mail, and pasted the description below.
> > I would be delighted to see this module incorperated into BioPerl if
> > appropriate. I don't know whether it will solve Hekki's problem, but may 
> > provide an alternative to writing a new serialiser!
> > 
> > Regards,
> > 
> > Will
> > 
> > ---
> > Will Spooner                   whs at sanger.ac.uk
> > Ensembl Web Developer    http://www.ensembl.org
> > 
> > 
> > NAME
> >   Bio::Root::Storable - object serialisation methods
> > 
> > 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.
> > 
> >   Currently stores objects in binary format (using the Perl Storable
> >   module). This can cause problems when storing and retrieving with different
> >   versions of Storable (e.g. on different machines). An ASCII storage
> >   option (using Data::Dumper) may be implemented in the future.
> > 
> >   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.
> > 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>