MySQLChecksum.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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.
 
=cut
 
package XrefMapper::Methods::MySQLChecksum;
 
use strict;
use warnings;
use Bio::EnsEMBL::DBSQL::DBConnection;
 
use base qw/XrefMapper::Methods::ChecksumBasic/;
 
use Bio::EnsEMBL::Utils::Exception qw(throw);
 
my $CHECKSUM_SQL = <<SQL;
select accession
from checksum_xref
where checksum =?
and source_id=?
SQL
 
sub perform_mapping {
  my ($self, $sequences, $source_id, $object_type, $db_url) = @_;
  
  my @final_results;
  my $dbc;
  if (defined $db_url) {
    my ($dbconn_part, $driver, $user, $pass, $host, $port, $dbname, $table_name, $tparam_name, $tparam_value, $conn_param_string) =
            $db_url =~ m{^((\w*)://(?:(\w+)(?:\:([^/\@]*))?\@)?(?:([\w\-\.]+)(?:\:(\d*))?)?/([\w\-\.]*))(?:/(\w+)(?:\?(\w+)=([\w\[\]\{\}]*))?)?((?:;(\w+)=(\w+))*)$};
    $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(
      -dbname => $dbname,
      -user => $user,
      -pass => $pass,
      -host => $host,
      -port => $port);
  } else {
    $dbc = $self->mapper()->xref()->dbc();
  }
  
  $dbc->sql_helper()->batch(-SQL => $CHECKSUM_SQL, -CALLBACK => sub {
    my ($sth) = @_;
    foreach my $sequence (@{$sequences}) {
      my $checksum = uc($self->md5_checksum($sequence));
      $sth->execute($checksum, $source_id);
      my $upi;
      while(my $row = $sth->fetchrow_arrayref()) {
        my ($local_upi) = @{$row};
        if(defined $upi) {
          throw sprintf('The sequence %s had a checksum of %s but this resulted in more than one UPI: [%s, %s]', $sequence->id(), $checksum, $upi, $local_upi);
        }
        $upi = $local_upi;
      }
      if(defined $upi){
        push(@final_results, { id => $sequence->id(), upi => $upi, object_type => $object_type });
      }
    }
    return;
  });
  
  return \@final_results;
}