[Bioperl-l] Re: cloning and Storable
Heikki Lehvaslaiho
heikki at ebi.ac.uk
Fri Sep 5 14:04:48 EDT 2003
Will,
Your quick! I merged your next version into the committed one. Hopefully
everything is fine. The test logic seems to be OK but it would be great
to get confirmation that all tests pass from someone without Storable.
-Heikki
On Fri, 2003-09-05 at 18:10, Will Spooner wrote:
> On Fri, 5 Sep 2003, Heikki Lehvaslaiho wrote:
>
> > Will,
> >
> > We are claiming to support perl 5.005 and luckily it was the first perl
> > release that contained Data::Dumper in core, so go ahead and add it. You
> > could use it as the default storage method as it is guarantied to be
> > present.
>
> Data::Dumper is a great debug tool, but has it's little ...problems...
>
> Now solved though - new code goes with Storable if it can, but uses
> Data::Dumper as a fallback. Users can set $Bio::Root::Storable::BINARY to
> false to force the use of Data::Dumper.
>
> Have mailed the latest module + test seperately.
>
> >
> > How do I know? RpmFind has info about all the rpms for a the past few
> > years. Here is a list of 5.005 modules:
> >
> > http://fr2.rpmfind.net//linux/RPM/redhat/6.2/i386/perl-5.00503-10.i386.html
>
> Thats a good trick ;)
>
> Will
>
>
>
>
>
> >
> > -Heikki
> >
> > On Fri, 2003-09-05 at 15:16, Will Spooner wrote:
> > > 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
> > > > ___ _/_/_/_/_/________________________________________________________
> > > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > --
> > ______ _/ _/_____________________________________________________
> > _/ _/ 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
> > ___ _/_/_/_/_/________________________________________________________
> >
>
>
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--
______ _/ _/_____________________________________________________
_/ _/ 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
___ _/_/_/_/_/________________________________________________________
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