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Unverified Commit 3d5e0050 authored by Kieron Taylor's avatar Kieron Taylor Committed by GitHub
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Merge pull request #358 from markmcdowall/feature/prepare_cached 

Added prepare_cached as a wrapper to the DBConnect.pm module
parents a03b0180 843b2c3c
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modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+ 99
− 54
View file @ 3d5e0050
......@@ -85,10 +85,10 @@ use Bio::EnsEMBL::Utils::SqlHelper;
Arg [DBNAME] : (optional) string
The name of the database to connect to.
Arg [HOST] : (optional) string
The domain name of the database host to connect to.
'localhost' by default.
The domain name of the database host to connect to.
'localhost' by default.
Arg [USER] : string
The name of the database user to connect with
The name of the database user to connect with
Arg [PASS] : (optional) string
The password to be used to connect to the database
Arg [PORT] : (optional) int
......@@ -111,16 +111,16 @@ use Bio::EnsEMBL::Utils::SqlHelper;
Arg [WAIT_TIMEOUT]: (optional) integer
Time in seconds for the wait timeout to happen. Time after which
the connection is deleted if not used. By default this is 28800 (8 hours)
on most systems.
on most systems.
So set this to greater than this if your connection are getting deleted.
Only set this if you are having problems and know what you are doing.
Arg [RECONNECT_WHEN_CONNECTION_LOST]: (optional) boolean
In case you're reusing the same database connection, i.e. DISCONNECT_WHEN_INACTIVE is
set to false and running a job which takes a long time to process (over 8hrs),
which means that the db connection may be lost, set this option to true.
On each prepare or do statement the db handle will be pinged and the database
In case you're reusing the same database connection, i.e. DISCONNECT_WHEN_INACTIVE is
set to false and running a job which takes a long time to process (over 8hrs),
which means that the db connection may be lost, set this option to true.
On each prepare or do statement the db handle will be pinged and the database
connection will be reconnected if it's lost.
Example : $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new
(-user => 'anonymous',
-dbname => 'homo_sapiens_core_20_34c',
......@@ -232,7 +232,7 @@ sub new {
=head2 connect
Example : $dbcon->connect()
Description: Connects to the database using the connection attribute
Description: Connects to the database using the connection attribute
information.
Returntype : none
Exceptions : none
......@@ -347,7 +347,7 @@ sub query_count {
=cut
sub equals {
my ( $self, $dbc ) = @_;
return 0 if ! defined $dbc;
......@@ -355,14 +355,14 @@ sub equals {
my $undef_str = q{!-undef-!};
my $undef_num = -1;
$return = 1 if (
$return = 1 if (
(($self->host() || $undef_str) eq ($dbc->host() || $undef_str)) &&
(($self->dbname() || $undef_str) eq ($dbc->dbname() || $undef_str)) &&
(($self->port() || $undef_num) == ($dbc->port() || $undef_num)) &&
(($self->username() || $undef_str) eq ($dbc->username() || $undef_str)) &&
($self->driver() eq $dbc->driver())
);
return $return;
}
......@@ -396,8 +396,8 @@ sub driver {
the TCP or UDP port to use to connect to the database
Example : $port = $db_connection->port();
Description: Getter / Setter for the port this connection uses to communicate
to the database daemon. There currently is no point in
setting this value after the connection has already been
to the database daemon. There currently is no point in
setting this value after the connection has already been
established by the constructor.
Returntype : string
Exceptions : none
......@@ -420,11 +420,11 @@ sub port {
=head2 dbname
Arg [1] : (optional) string $arg
The new value of the database name used by this connection.
The new value of the database name used by this connection.
Example : $dbname = $db_connection->dbname()
Description: Getter/Setter for the name of the database used by this
Description: Getter/Setter for the name of the database used by this
connection. There is currently no point in setting this value
after the connection has already been established by the
after the connection has already been established by the
constructor.
Returntype : string
Exceptions : none
......@@ -444,11 +444,11 @@ sub dbname {
=head2 username
Arg [1] : (optional) string $arg
The new value of the username used by this connection.
The new value of the username used by this connection.
Example : $username = $db_connection->username()
Description: Getter/Setter for the username used by this
Description: Getter/Setter for the username used by this
connection. There is currently no point in setting this value
after the connection has already been established by the
after the connection has already been established by the
constructor.
Returntype : string
Exceptions : none
......@@ -467,7 +467,7 @@ sub username {
=head2 user
Arg [1] : (optional) string $arg
The new value of the username used by this connection.
The new value of the username used by this connection.
Example : $user = $db_connection->user()
Description: Convenience alias for the username method
Returntype : String
......@@ -483,11 +483,11 @@ sub user {
=head2 host
Arg [1] : (optional) string $arg
The new value of the host used by this connection.
The new value of the host used by this connection.
Example : $host = $db_connection->host()
Description: Getter/Setter for the domain name of the database host use by
this connection. There is currently no point in setting
this value after the connection has already been established
Description: Getter/Setter for the domain name of the database host use by
this connection. There is currently no point in setting
this value after the connection has already been established
by the constructor.
Returntype : string
Exceptions : none
......@@ -506,7 +506,7 @@ sub host {
=head2 hostname
Arg [1] : (optional) string $arg
The new value of the host used by this connection.
The new value of the host used by this connection.
Example : $hostname = $db_connection->hostname()
Description: Convenience alias for the host method
Returntype : String
......@@ -553,7 +553,7 @@ sub password {
=head2 pass
Arg [1] : (optional) string $arg
The new value of the password used by this connection.
The new value of the password used by this connection.
Example : $pass = $db_connection->pass()
Description: Convenience alias for the password method
Returntype : String
......@@ -600,9 +600,9 @@ sub disconnect_when_inactive {
Arg [1] : (optional) boolean $newval
Example : $db->reconnect_when_lost(1);
Description: Getter/Setter for the reconnect_when_lost flag. If set
to true the db handle will be pinged on each prepare or do statement
to true the db handle will be pinged on each prepare or do statement
and the connection will be reestablished in case it's lost.
Useful for long running jobs (over 8hrs), which means that the db
Useful for long running jobs (over 8hrs), which means that the db
connection may be lost.
Returntype : boolean
Exceptions : none
......@@ -650,7 +650,7 @@ sub locator {
=head2 db_handle
Arg [1] : DBI Database Handle $value
Example : $dbh = $db_connection->db_handle()
Example : $dbh = $db_connection->db_handle()
Description: Getter / Setter for the Database handle used by this
database connection.
Returntype : DBI Database Handle
......@@ -698,7 +698,7 @@ sub prepare {
}
#warn "SQL(".$self->dbname."):" . join(' ', @args) . "\n";
if ( ($self->reconnect_when_lost()) and (!$self->db_handle()->ping()) ) {
if ( ($self->reconnect_when_lost()) and (!$self->db_handle()->ping()) ) {
$self->reconnect();
}
my $sth = $self->db_handle->prepare(@args);
......@@ -713,10 +713,55 @@ sub prepare {
return $sth;
}
=head2 prepare_cached
Arg [1] : string $string
the SQL statement to prepare
Example : $sth = $db_connection->prepare_cached("SELECT column FROM table");
Description: Prepares a SQL statement using the internal DBI database handle
and returns the DBI statement handle. The prepared statement is
cached so that it does not have to be prepared again.
If only a subset of rows are required, finish() should be called
on the object to free up the statement handle.
For further information please consult https://metacpan.org/pod/DBI#prepare_cached
Returntype : DBI statement handle
Exceptions : thrown if the SQL statement is empty, or if the internal
database handle is not present
Caller : Adaptor modules
Status : Experimental
=cut
sub prepare_cached {
my ($self, @args) = @_;
if( ! $args[0] ) {
throw("Attempting to prepare_cached an empty SQL query.");
}
if ( ( $self->reconnect_when_lost() ) and ( !$self->db_handle()->{Active} ) ) {
$self->reconnect();
}
my $sth = $self->db_handle->prepare_cached( @args );
# return an overridden statement handle that provides us with
# the means to disconnect inactive statement handles automatically
bless $sth, "Bio::EnsEMBL::DBSQL::StatementHandle";
$sth->dbc( $self );
$sth->sql( $args[0] );
$self->query_count( $self->query_count() + 1 );
return $sth;
}
=head2 reconnect
Example : $dbcon->reconnect()
Description: Reconnects to the database using the connection attribute
Description: Reconnects to the database using the connection attribute
information if db_handle no longer pingable.
Returntype : none
Exceptions : none
......@@ -757,16 +802,16 @@ sub do {
# warn "SQL(".$self->dbname."): $string";
my $error;
my $do_result = $self->work_with_db_handle(sub {
my ($dbh) = @_;
my $result = eval { $dbh->do($string, $attr, @bind_values) };
$error = $@ if $@;
return $result;
});
throw "Detected an error whilst executing statement '$string': $error" if $error;
return $do_result;
}
......@@ -777,7 +822,7 @@ sub do {
Description: Gives access to the DBI handle to execute methods not normally
provided by the DBConnection interface
Returntype : Any from callback
Exceptions : If the callback paramater is not a CodeRef; all other
Exceptions : If the callback paramater is not a CodeRef; all other
errors are re-thrown after cleanup.
Caller : Adaptor modules
Status : Stable
......@@ -788,12 +833,12 @@ sub work_with_db_handle {
my ($self, $callback) = @_;
my $wantarray = wantarray;
assert_ref($callback, 'CODE', 'callback');
if( $self->reconnect_when_lost() && !$self->db_handle()->ping()) {
if( $self->reconnect_when_lost() && !$self->db_handle()->ping()) {
$self->reconnect();
}
my @results;
eval {
if($wantarray) {
if($wantarray) {
@results = $callback->($self->db_handle())
}
elsif(defined $wantarray) {
......@@ -804,7 +849,7 @@ sub work_with_db_handle {
}
};
my $original_error = $@;
$self->query_count($self->query_count()+1);
eval {
if($self->disconnect_when_inactive()) {
......@@ -817,7 +862,7 @@ sub work_with_db_handle {
if($original_error) {
throw "Detected an error when running DBI wrapper callback:\n$original_error";
}
if(defined $wantarray) {
return ($wantarray) ? @results : $results[0];
}
......@@ -832,11 +877,11 @@ sub work_with_db_handle {
duration of the callback. This is very useful if you need
to make multiple database calls avoiding excessive database
connection creation/destruction but still want the API
to disconnect after the body of work.
to disconnect after the body of work.
The value of C<disconnect_when_inactive()> is set to 0 no
matter what the original value was & after $callback has
been executed. If C<disconnect_when_inactive()> was
been executed. If C<disconnect_when_inactive()> was
already set to 0 then this method will be an effective no-op.
Returntype : None
Exceptions : Raised if there are issues with reverting the connection to its
......@@ -854,7 +899,7 @@ sub prevent_disconnect {
eval { $callback->(); };
my $original_error = $@;
eval {
$self->disconnect_when_inactive($original_dwi);
$self->disconnect_when_inactive($original_dwi);
};
if($@) {
warning "Detected an error whilst attempting to reset disconnect_when_idle: $@";
......@@ -897,7 +942,7 @@ sub quote_identifier {
Arg [1] : none
Example : $dbc->disconnect_if_idle();
Description: Disconnects from the database if there are no currently active
statement handles.
statement handles.
It is called automatically by the DESTROY method of the
Bio::EnsEMBL::DBSQL::SQL::StatementHandle if the
disconect_when_inactive flag is set.
......@@ -935,7 +980,7 @@ sub disconnect_if_idle {
" activekids=",$db_handle->{ActiveKids},"\n");
return 1;
}
$db_handle->disconnect();
$self->connected(undef);
$self->disconnect_count($self->disconnect_count()+1);
......@@ -950,9 +995,9 @@ sub disconnect_if_idle {
Arg [1] : string $sql
Arg [2] : int $max_number
Example : my $new_sql = $dbc->add_limit_clause($sql,$max_number);
Description: Giving an SQL statement, it adds a limit clause, dependent on the database
(in MySQL, should add a LIMIT at the end, MSSQL uses a TOP clause)
Returntype : String containing the new valid SQL statement
Description: Giving an SQL statement, it adds a limit clause, dependent on the database
(in MySQL, should add a LIMIT at the end, MSSQL uses a TOP clause)
Returntype : String containing the new valid SQL statement
Exceptions : none
Caller : general
Status : at risk
......@@ -986,7 +1031,7 @@ sub add_limit_clause{
Arg [1] : date $date
Example : my $string = $dbc->from_date_to_seconds($date);
Description: Giving a string representing a column of type date
Description: Giving a string representing a column of type date
applies the database function to convert to the number of seconds from 01-01-1970
Returntype : string
Exceptions : none
......@@ -1005,7 +1050,7 @@ sub from_date_to_seconds{
Arg [1] : int $seconds
Example : my $string = $dbc->from_seconds_to_date($seconds);
Description: Giving an int representing number of seconds
applies the database function to convert to a date
applies the database function to convert to a date
Returntype : string
Exceptions : none
Caller : general
......@@ -1049,13 +1094,13 @@ sub sql_helper {
Example : my $hash = $dbc->to_hash();
my $new_dbc = $dbc->new(%{$hash});
Description: Provides a hash which is compatible with the
Description: Provides a hash which is compatible with the
parameters for DBConnection's new() method. This can be
useful during serialisation
Returntype : Hash
Exceptions : none
Caller : general
Status : New
Status : New
=cut
......
modules/t/dbConnection.t
+ 11
− 0
View file @ 3d5e0050
......@@ -114,6 +114,17 @@ is_deeply($dbc->to_hash(), \%dbc_args, 'Checking to_hash() can roundtrip a DBCon
$sth->finish;
}
{
#
# 12 prepare_cached
#
my $sth = $dbc->prepare_cached('SELECT gene_id, biotype FROM gene LIMIT 1');
$sth->execute;
my @row = $sth->fetchrow_array;
ok($sth->rows, "prepare_cached");
$sth->finish;
}
#
# try the database with the disconnect_when_inactive flag set.
# this should automatically disconnect from the db
......
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