view variant_effect_predictor/Bio/EnsEMBL/DBSQL/StatementHandle.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::StatementHandle

=head1 SYNOPSIS

Do not use this class directly.  It will automatically be used by the
Bio::EnsEMBL::DBSQL::DBConnection class.

=head1 DESCRIPTION

This class extends DBD::mysql::st so that the DESTROY method may be
overridden.  If the DBConnection::disconnect_when_inactive flag is set
this statement handle will cause the database connection to be closed
when it goes out of scope and there are no other open statement handles.

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::StatementHandle;

use vars qw(@ISA);
use strict;

use Bio::EnsEMBL::Utils::Exception qw(warning throw);

use DBI;

#use Time::HiRes qw(time);

@ISA = qw(DBI::st);


# As DBD::mysql::st is a tied hash can't store things in it,
# so have to have parallel hash
my %dbchash;
my %dbc_sql_hash;


sub dbc {
  my $self = shift;

  if (@_) {
    my $dbc = shift;
    if(!defined($dbc)) {
      # without delete key space would grow indefinitely causing mem-leak
      delete($dbchash{$self});
    } else {
      $dbchash{$self} = $dbc;
    }
  }

  return $dbchash{$self};
}

sub sql {
  my $self = shift;

  if (@_) {
    my $sql = shift;
    if(!defined($sql)) {
      # without delete key space would grow indefinitely causing mem-leak
      delete($dbc_sql_hash{$self});
    } else {
      $dbc_sql_hash{$self} = $sql;
    }
  }

  return $dbc_sql_hash{$self};
}

sub DESTROY {
  my ($self) = @_;

  my $dbc = $self->dbc;
  $self->dbc(undef);
  my $sql = $self->sql;
  $self->sql(undef);

  # Re-bless into DBI::st so that superclass destroy method is called if
  # it exists (it does not exist in all DBI versions).
  bless( $self, 'DBI::st' );

  # The count for the number of kids is decremented only after this
  # function is complete. Disconnect if there is 1 kid (this one)
  # remaining.
  if (    $dbc
       && $dbc->disconnect_when_inactive()
       && $dbc->connected
       && ( $dbc->db_handle->{Kids} == 1 ) )
  {
    if ( $dbc->disconnect_if_idle() ) {
      warn("Problem disconnect $self around sql = $sql\n");
    }
  }
} ## end sub DESTROY

1;

# Comment out this "__END__" for printing out handy debug information
# (every query if you want).

__END__

# To stop caching messing up your timings, try doing the following on
# any adapter:
#
#   $slice_adaptor->dbc()->db_handle()
#       ->do("SET SESSION query_cache_type = OFF");
#
# To start logging:
# Bio::EnsEMBL::DBSQL::StatementHandle->sql_timing_start();
#
# To display the results:
# Bio::EnsEMBL::DBSQL::StatementHandle->sql_timing_print(1);
#
# To pause logging:
# Bio::EnsEMBL::DBSQL::StatementHandle->sql_timimg_pause();
#
# To resume logging after pause:
# Bio::EnsEMBL::DBSQL::StatementHandle->sql_timimg_resume();

use Time::HiRes qw(time);

my @bind_args = ();
my $dump      = 0;
my %total_time;
my %min_time;
my %max_time;
my %number_of_times;
my %first_time;
my $grand_total;

sub sql_timing_start {
  %total_time      = ();
  %number_of_times = ();
  %min_time        = ();
  %max_time        = ();
  %first_time      = ();
  $dump            = 1;
}

sub sql_timing_pause  { $dump = 0 }
sub sql_timing_resume { $dump = 1 }

sub sql_timing_print {
  my ( $self, $level, $fh ) = @_;

  my $grand_total = 0;

  if ( !defined($fh) ) {
    $fh = \*STDERR;
  }

  print( ref($fh), "\n" );

  foreach my $key ( keys %total_time ) {
    $grand_total += $total_time{$key};

    if ( !( defined($level) and $level ) ) { next }

    print( $fh $key, "\n" );

    print( $fh
        "total\t \tnum\tfirst \t\tavg\t \t[min     ,max      ]\n" );

    printf( $fh "%6f\t%d\t%6f\t%6f\t[%6f, %6f]\n\n",
      $total_time{$key}, $number_of_times{$key},
      $first_time{$key}, ( $total_time{$key}/$number_of_times{$key} ),
      $min_time{$key}, $max_time{$key} );
  }

  printf( $fh "\ntotal time %6f\n\n", $grand_total );

} ## end sub sql_timing_print

sub bind_param {
  my ( $self, @args ) = @_;

  $bind_args[ $args[0] - 1 ] = $args[1];
  $self->SUPER::bind_param(@args);
}

sub execute {
  my ( $self, @args ) = @_;

  my $retval;
  # Skip dumping if !$dump
  if ( !$dump ) {
      local $self->{RaiseError};
      $retval = $self->SUPER::execute(@args);
      if ( !defined($retval) ) {
        throw("Failed to execute SQL statement");
      }
      return $retval;
  }

  my $sql = $self->sql();
  my @chrs = split( //, $sql );

  my $j = 0;

  for ( my $i = 0; $i < @chrs; $i++ ) {
    if ( $chrs[$i] eq '?' && defined( $bind_args[$j] ) ) {
      $chrs[$i] = $bind_args[ $j++ ];
    }
  }

  my $str = join( '', @chrs );

  # Uncomment this line if you want to see sql in order.
  # print( STDERR "\n\nSQL:\n$str\n\n" );

  my $time = time();
  {
    local $self->{RaiseError};
    $retval = $self->SUPER::execute(@args);
    if ( !defined($retval) ) {
      throw("Failed to execute SQL statement");
    }
  }
  #  my $res  = $self->SUPER::execute(@args);
  $time = time() - $time;

  if ( defined( $total_time{$sql} ) ) {
    $total_time{$sql} += $time;
    $number_of_times{$sql}++;

    if ( $min_time{$sql} > $time ) { $min_time{$sql} = $time }
    if ( $max_time{$sql} < $time ) { $max_time{$sql} = $time }

  } else {
    $first_time{$sql}      = $time;
    $max_time{$sql}        = $time;
    $min_time{$sql}        = $time;
    $total_time{$sql}      = $time;
    $number_of_times{$sql} = 1;
  }

  return $retval;
} ## end sub execute

1;