Bio::DB::GFF::Adaptor::dbi
caching_handle
Toolbar
Summary
Bio::DB::GFF::Adaptor::dbi::caching_handle -- Cache for database handles
Package variables
Globals (from "use vars" definitions)
$AUTOLOAD
Included modules
Inherit
Synopsis
use Bio::DB::GFF::Adaptor::dbi::caching_handle;
$db = Bio::DB::GFF::Adaptor::dbi::caching_handle->new('dbi:mysql:test');
$sth = $db->prepare('select * from foo');
@h = $sth->fetch_rowarray;
$sth->finish
Description
This module handles a pool of database handles. It was motivated by
the MYSQL driver's {mysql_use_result} attribute, which dramatically
improves query speed and memory usage, but forbids additional query
statements from being evaluated while an existing one is in use.
This module is a plug-in replacement for vanilla DBI. It
automatically activates the {mysql_use_result} attribute for the mysql
driver, but avoids problems with multiple active statement handlers by
creating new database handles as needed.
Methods
Methods description
Title : attribute
Usage : $value = $db->attribute(AttributeName , [$newvalue])
Function: get/set DBI::db handle attribute
Returns : current state of the attribute
Args : name of the attribute and optional new setting of attribute
Status : public
Under Bio::DB::GFF::Adaptor::dbi::caching_handle the DBI::db
attributes that are usually set using hashref calls are unavailable.
Use attribute() instead. For example, instead of:
$dbh->{AutoCommit} = 0;
use
$dbh->attribute(AutoCommit=>0); |
Title : dbi_quote
Usage : $string = $db->dbi_quote($sql,@args)
Function: perform bind variable substitution
Returns : query string
Args : the query string and bind arguments
Status : public
This method replaces the bind variable "?" in a SQL statement with
appropriately quoted bind arguments. It is used internally to handle
drivers that don't support argument binding. |
Title : debug
Usage : $debug = $db->debug([$debug])
Function: activate debugging messages
Returns : current state of flag
Args : optional new setting of flag
Status : public |
Title : do_query
Usage : $sth = $db->do_query($query,@args)
Function: perform a DBI query
Returns : a statement handler
Args : query string and list of bind arguments
Status : Public
This method performs a DBI prepare() and execute(), returning a
statement handle. You will typically call fetch() of fetchrow_array()
on the statement handle. The parsed statement handle is cached for
later use. |
Methods code
sub AUTOLOAD
{ my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/;
return if $func_name eq 'DESTROY';
my $self = shift or return DBI->$func_name(@_);
$self->dbh->$func_name(@_); } | sub attribute
{ my $self = shift;
my $dbh = $self->dbh->{dbh};
return $dbh->{$_[0]} = $_[1] if @_ == 2;
return $dbh->{$_[0]} if @_ == 1;
return;} | sub dbh
{ my $self = shift;
foreach (@{$self->{dbh}}) {
return $_ if $_->inuse == 0;
}
warn "(Re)connecting to database\n" if $self->debug;
my $dbh = DBI->connect(@{$self->{args}}) or return;
$dbh->{PrintError} = 0;
$dbh->{LongReadLen} = 100*65535;
$dbh->{LongTruncOk} = 0;
my $wrapper = Bio::DB::GFF::Adaptor::dbi::faux_dbh->new($dbh);
push @{$self->{dbh}},$wrapper;
$wrapper;} | sub dbi_quote
{ my $self = shift;
my ($query,@args) = @_;
my $dbh = $self->dbh;
$query =~ s/\?/$dbh->quote(shift @args)/eg;
$query;
}
package Bio::DB::GFF::Adaptor::dbi::faux_dbh;
use vars '$AUTOLOAD'; } | sub debug
{ my $self = shift;
my $d = $self->{debug};
$self->{debug} = shift if @_;
$d;} | sub disconnect
{ my $self = shift;
$_ && $_->disconnect foreach @{$self->{dbh}};
$self->{dbh} = [];} | sub do_query
{ my $self = shift;
my ($query,@args) = @_;
warn $self->dbi_quote($query,@args),"\n" if $self->debug;
my $sth = $self->prepare($query);
$sth->execute(@args) || $self->throw("Couldn't execute query $query:\n ".DBI->errstr."\n");
$sth;} | sub new
{ my $class = shift;
my @dbi_args = @_;
my $self = bless {
dbh => [],
args =>\@ dbi_args,
debug => 0,
},$class;
$self->dbh || $self->throw("Can't connect to database: " . DBI->errstr);
$self;} | sub prepare
{ my $self = shift;
my $query = shift;
my $dbh = $self->dbh || $self->throw("Can't connect to database: " . DBI->errstr);
if (my $sth = $self->{$dbh}{$query}) {
warn "Using cached statement handler\n" if $self->debug;
return $sth;
} else {
warn "Creating new statement handler\n" if $self->debug;
$sth = $dbh->prepare($query) || $self->throw("Couldn't prepare query $query:\n ".DBI->errstr."\n");
return $self->{$dbh}{$query} = $sth;
} } | General documentation
The object constructor is
Bio::DB::GFF::Adaptor::dbi::caching_handle->new(). This is called
like DBI->connect() and takes the same arguments. The returned object
looks and acts like a conventional database handle.
In addition to all the standard DBI handle methods, this package adds
the following: