AccumulatorAdaptor.pm 2.82 KB
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=pod

=head1 NAME

    Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor

=head1 SYNOPSIS

    $dba->get_AccumulatorAdaptor->store( \@rows );

=head1 DESCRIPTION

    This is currently an "objectless" adaptor for building accumulated structures.

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=head1 LICENSE

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    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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    Copyright [2016-2020] EMBL-European Bioinformatics Institute
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    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.

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=head1 CONTACT

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    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
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=cut


package Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor;

use strict;
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use warnings;
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use Bio::EnsEMBL::Hive::Utils ('destringify');

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


sub default_table_name {
    return 'accu';
}


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sub fetch_structures_for_job_ids {
    my ($self, $job_ids_csv, $id_scale, $id_offset) = @_;
    $id_scale   ||= 1;
    $id_offset  ||= 0;
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    my %structures = ();

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    if( $job_ids_csv ) {

        my $sql = "SELECT receiving_job_id, struct_name, key_signature, value FROM accu WHERE receiving_job_id in ($job_ids_csv)";
        my $sth = $self->prepare( $sql );
        $sth->execute();

        ROW: while(my ($receiving_job_id, $struct_name, $key_signature, $stringified_value) = $sth->fetchrow_array() ) {

            my $value = destringify($stringified_value);

            my $sptr = \$structures{$receiving_job_id * $id_scale + $id_offset}{$struct_name};

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            while( $key_signature=~/(?:(?:\[(\d*)\])|(?:\{(.*?)\}))/g) {
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                my ($array_index, $hash_key) = ($1, $2);
                if(defined($array_index)) {
                    unless(length($array_index)) {
                        $array_index = scalar(@{$$sptr||[]});
                    }
                    $sptr = \$$sptr->[$array_index];
                } elsif(defined($hash_key)) {
                    if(length($hash_key)) {
                        $sptr = \$$sptr->{$hash_key};
                    } else {
                        $sptr = \$$sptr->{$value};
                        $$sptr++;
                        next ROW;
                    }
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                }
            }
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            $$sptr = $value;
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        }
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        $sth->finish;
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    }

    return \%structures;
}

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