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Commit 711a95b4 authored by Will Spooner's avatar Will Spooner
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Added daily result table in the same fassion as hit and hsp

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modules/Bio/EnsEMBL/External/BlastAdaptor.pm
+ 54
− 33
View file @ 711a95b4
......@@ -34,15 +34,6 @@ CREATE TABLE blast_ticket (
KEY update_time (update_time)
) TYPE=MyISAM";
our $SQL_CREATE_RESULT = "
CREATE TABLE blast_result (
result_id int(10) unsigned NOT NULL auto_increment,
ticket varchar(32) default NULL,
object longblob,
PRIMARY KEY (result_id),
KEY ticket (ticket)
) TYPE=MyISAM";
our $SQL_CREATE_TABLE_LOG = "
CREATE TABLE blast_table_log (
table_id int(10) unsigned NOT NULL auto_increment,
......@@ -60,6 +51,16 @@ CREATE TABLE blast_table_log (
KEY table_status (table_status)
) TYPE=MyISAM";
our $SQL_CREATE_DAILY_RESULT = "
CREATE TABLE %s (
result_id int(10) unsigned NOT NULL auto_increment,
ticket varchar(32) default NULL,
object longblob,
PRIMARY KEY (result_id),
KEY ticket (ticket)
) TYPE=MyISAM";
our $SQL_CREATE_DAILY_HIT = "
CREATE TABLE %s (
hit_id int(10) unsigned NOT NULL auto_increment,
......@@ -121,18 +122,18 @@ WHERE ticket = ? ";
#--- RESULTS ---
our $SQL_RESULT_STORE = "
INSERT INTO blast_result ( object, ticket )
INSERT INTO blast_result%s ( object, ticket )
VALUES ( ? , ? )";
our $SQL_RESULT_UPDATE = "
UPDATE blast_result
UPDATE blast_result%s
SET object = ?,
ticket = ?
WHERE result_id = ?";
our $SQL_RESULT_RETRIEVE = "
SELECT object
FROM blast_result
FROM blast_result%s
WHERE result_id = ? ";
#--- HITS ---
......@@ -289,26 +290,28 @@ sub store_result{
my $dbh = $self->db->db_handle;
my $ticket = $res->group_ticket;
my $token = $res->token;
my $store_obj = $res->_prepare_storable;
my $frozen = freeze( $store_obj );
my $ticket = $res->group_ticket;
my ( $id, $use_date ) = split( '!!', $res->token);
$use_date ||= $self->use_date('RESULT');
my $rv = 0;
if( $token ){
my $sth = $dbh->prepare( $SQL_RESULT_RETRIEVE );
$rv = $sth->execute( $token ) || $self->throw( $sth->errstr );
if( $id ){
my $sth = $dbh->prepare( sprintf $SQL_RESULT_RETRIEVE, $use_date );
$rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
$sth->finish;
}
if( $rv < 1 ){# Insert
my $sth = $dbh->prepare( $SQL_RESULT_STORE );
my $sth = $dbh->prepare( sprintf $SQL_RESULT_STORE, $use_date );
$sth->execute( $frozen, $ticket ) || $self->throw( $sth->errstr );
$res->token( $dbh->{mysql_insertid} );
my $id = $dbh->{mysql_insertid};
$res->token( join( '!!', $id, $use_date ) );
$sth->finish;
}
else{ # Update
my $sth = $dbh->prepare( $SQL_RESULT_UPDATE );
$sth->execute( $frozen, $ticket, $token ) || $self->throw( $sth->errstr );
my $sth = $dbh->prepare( sprintf $SQL_RESULT_UPDATE, $use_date );
$sth->execute( $frozen, $ticket, $id ) || $self->throw( $sth->errstr );
$sth->finish;
}
return $res->token();
......@@ -329,10 +332,12 @@ sub store_result{
sub retrieve_result{
my $self = shift;
my $id = shift || $self->throw( "Need a Result token" );
my $token = shift || $self->throw( "Need a Hit token" );
my ( $id, $use_date ) = split( '!!',$token);
$use_date ||= '';
my $dbh = $self->db->db_handle;
my $sth = $dbh->prepare( $SQL_RESULT_RETRIEVE );
my $sth = $dbh->prepare( sprintf $SQL_RESULT_RETRIEVE, $use_date );
my $rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
if( $rv < 1 ){ $self->throw( "Token $id not found" ) }
my ( $frozen ) = $sth->fetchrow_array;
......@@ -629,13 +634,13 @@ sub dynamic_use {
=cut
my %valid_table_types = ( HIT=>1, HSP=>1 );
my %valid_table_types = ( HIT=>1, HSP=>1, RESULT=>1 );
sub use_date {
my $key = '_current_table';
my $self = shift;
my $type = uc( shift );
$valid_table_types{$type} ||
$self->throw( "Need a table type (Hit or HSP)" );
$self->throw( "Need a table type (Result, Hit or HSP)" );
$self->{$key} ||= {};
if( ! $self->{$key}->{$type} ){
......@@ -747,7 +752,7 @@ WHERE ticket like "%s" /;
=head2 create_tables
Arg [1] : none
Function : Creates the blast_ticket, blast_result and blast_table_log
Function : Creates the blast_ticket and blast_table_log
tables in the database indicated by the database handle.
Checks first to make sure they do not exist
Returntype: boolean
......@@ -774,11 +779,6 @@ sub create_tables {
my $sth = $dbh->prepare( $SQL_CREATE_TICKET );
my $rv = $sth->execute() || $self->throw( $sth->errstr );
}
if( $rv_res == 0 ){
warn( "Creating blast_result table" );
my $sth = $dbh->prepare( $SQL_CREATE_RESULT );
my $rv = $sth->execute() || $self->throw( $sth->errstr );
}
if( $rv_log == 0 ){
warn( "Creating blast_result table" );
my $sth = $dbh->prepare( $SQL_CREATE_TABLE_LOG );
......@@ -792,8 +792,9 @@ sub create_tables {
=head2 rotate_daily_tables
Arg [1] : none
Function : Creates the daily blast_hit{date} and blast_hsp{date}
tables in the database indicated by the database handle.
Function : Creates the daily blast_result{date}, blast_hit{date}
and blast_hsp{date} tables in the database indicated by
the database handle.
Checks first to make sure they do not exist.
Sets the new table to 'CURRENT' in the blast_table_log.
Sets the previous 'CURRENT' table to filled.
......@@ -812,6 +813,7 @@ sub rotate_daily_tables {
my( $day, $month, $year ) = (localtime)[3,4,5];
my $date = sprintf( "%04d%02d%02d", $year+1900, $month+1, $day );
my $res_table = "blast_result$date";
my $hit_table = "blast_hit$date";
my $hsp_table = "blast_hsp$date";
......@@ -819,9 +821,28 @@ sub rotate_daily_tables {
my $q = 'show table status like ?';
my $sth = $dbh->prepare( $q );
my $rv_res = $sth->execute($res_table) || $self->throw($sth->errstr);
my $rv_hit = $sth->execute($hit_table) || $self->throw($sth->errstr);
my $rv_hsp = $sth->execute($hsp_table) || $self->throw($sth->errstr);
if( $rv_res == 0 ){
warn( "Creating today's $res_table table\n" );
# Create new table
my $q = sprintf($SQL_CREATE_DAILY_RESULT, $res_table);
my $sth = $dbh->prepare( $q );
my $rv = $sth->execute() || $self->throw( $sth->errstr );
# Flip current table in blast_table_tog
my $last_date = $self->use_date( "RESULT" ) || '';
my $sth2 = $dbh->prepare( $SQL_TABLE_LOG_INSERT );
my $sth3 = $dbh->prepare( $SQL_TABLE_LOG_UPDATE );
$sth2->execute( "$res_table",'CURRENT','RESULT',$date )
|| die( $self->throw( $sth2->errstr ) );
$sth3->execute( 'FILLED','0',0,"blast_result$last_date")
|| die( $self->throw( $sth3->errstr ) );
}
if( $rv_hit == 0 ){
warn( "Creating today's $hit_table table\n" );
......
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