ObjectAdaptor.pm 2.5 KB
Newer Older
1 2 3 4
=pod

=head1 NAME

5
    Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor
6 7 8 9 10 11 12 13 14 15 16

=head1 SYNOPSIS

    $object_adaptor = $dba->get_SpecificObjectAdaptor;
    $object_adaptor = $specific_object->adaptor;

=head1 DESCRIPTION

    This module defines a parent class for all specific object adaptors.
    It is not supposed to be instantiated directly.

17 18
=head1 LICENSE

19
    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
20 21 22 23 24 25 26 27 28 29

    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

         http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.

30 31
=head1 CONTACT

32
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

=cut


package Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor;

use strict;

use base ('Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor');


sub object_class {
    die "Please define object_class() in your specific adaptor class to return the class name of your intended object";
}


sub slicer {    # take a slice of the object (if only we could inline in Perl!)
    my ($self, $object, $fields) = @_;

52 53 54
    my $autoinc_id = $self->autoinc_id();

    return [ map { ($_ eq $autoinc_id) ? $object->dbID() : $object->$_() } @$fields ];
55 56 57 58 59 60
}


sub objectify { # turn the hashref into an object (if only we could inline in Perl!)
    my ($self, $hashref) = @_;

61 62 63
    my $autoinc_id = $self->autoinc_id();

    return $self->object_class()->new( -adaptor => $self, map { ('-'.uc( ($_ eq $autoinc_id) ? 'dbID' : $_ ) => $hashref->{$_}) } keys %$hashref );
64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91
}


sub mark_stored {
    my ($self, $object, $dbID) = @_;

    if($self->autoinc_id()) {
        $object->dbID($dbID);
    }
    $object->adaptor($self);
}


sub create_new {
    my $self = shift @_;

    my $check_presence_in_db_first = (scalar(@_)%2)
        ? pop @_    # extra 'odd' parameter that would disrupt the hash integrity anyway
        : 0;        # do not check by default

    my $object = $self->object_class()->new( -adaptor => $self, @_ );

    return $self->store( $object, $check_presence_in_db_first );
}


1;