diff --git a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
index 61ac03f23f9ed05d5b613d0fce4d14ee287c5208..4e40198bbc4a24c26ef4000da7b748023d605077 100644
--- a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
+++ b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
@@ -5,16 +5,176 @@ use strict;
use DBI;
use Storable qw(freeze thaw);
use Data::Dumper qw( Dumper );
+use Time::Local;
use vars qw(@ISA);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::DBSQL::DBConnection;
-#use Bio::Search::HSP::EnsemblHSP; # This is a web module
+use Bio::Search::HSP::EnsemblHSP; # This is a web module
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
#@ISA = qw( Bio::EnsEMBL::DBSQL::DBConnection );
+
+#----------------------------------------------------------------------
+# Define SQL
+
+#--- CREATE TABLES ---
+our $SQL_CREATE_TICKET = "
+CREATE TABLE blast_ticket (
+ ticket_id int(10) unsigned NOT NULL auto_increment,
+ create_time datetime NOT NULL default '0000-00-00 00:00:00',
+ update_time datetime NOT NULL default '0000-00-00 00:00:00',
+ ticket varchar(32) NOT NULL default '',
+ status enum('CURRENT','DELETED') NOT NULL default 'CURRENT',
+ object longblob,
+ PRIMARY KEY (ticket_id),
+ UNIQUE KEY ticket (ticket),
+ KEY create_time (create_time),
+ KEY update_time (update_time)
+) TYPE=MyISAM";
+
+our $SQL_CREATE_TABLE_LOG = "
+CREATE TABLE blast_table_log (
+ table_id int(10) unsigned NOT NULL auto_increment,
+ table_name varchar(32),
+ table_type enum('TICKET','RESULT','HIT','HSP') default NULL,
+ table_status enum('CURRENT','FILLED','DELETED') default NULL,
+ use_date date default NULL,
+ create_time datetime default NULL,
+ delete_time datetime default NULL,
+ num_objects int(10) default NULL,
+ PRIMARY KEY (table_id),
+ KEY table_name (table_name),
+ KEY table_type (table_type),
+ KEY use_date (use_date),
+ 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,
+ ticket varchar(32) default NULL,
+ object longblob,
+ PRIMARY KEY (hit_id),
+ KEY ticket (ticket)
+) TYPE=MyISAM";
+
+our $SQL_CREATE_DAILY_HSP = "
+CREATE TABLE %s (
+ hsp_id int(10) unsigned NOT NULL auto_increment,
+ ticket varchar(32) default NULL,
+ object longblob,
+ chr_name varchar(32) default NULL,
+ chr_start int(10) unsigned default NULL,
+ chr_end int(10) unsigned default NULL,
+ PRIMARY KEY (hsp_id),
+ KEY ticket (ticket)
+) TYPE=MyISAM MAX_ROWS=705032704 AVG_ROW_LENGTH=4000";
+
+#--- TABLE LOG ---
+our $SQL_SELECT_TABLE_LOG_CURRENT = "
+SELECT use_date
+FROM blast_table_log
+WHERE table_type = ?
+AND table_status = 'CURRENT'
+ORDER BY use_date DESC";
+
+our $SQL_TABLE_LOG_INSERT = "
+INSERT into blast_table_log
+ ( table_name, table_status, table_type, use_date, create_time)
+VALUES ( ?, ?, ?, ?, NOW() )";
+
+our $SQL_TABLE_LOG_UPDATE = "
+UPDATE blast_table_log
+SET table_status = ?,
+ delete_time = ?,
+ num_objects = ?
+WHERE table_name = ?";
+
+#--- TICKETS ---
+
+our $SQL_SEARCH_MULTI_STORE = "
+INSERT INTO blast_ticket ( create_time, update_time, object, ticket )
+VALUES ( NOW(), NOW(), ? , ? )";
+
+our $SQL_SEARCH_MULTI_UPDATE = "
+UPDATE blast_ticket
+SET object = ?,
+ update_time = NOW()
+WHERE ticket = ?";
+
+our $SQL_SEARCH_MULTI_RETRIEVE = "
+SELECT object
+FROM blast_ticket
+WHERE ticket = ? ";
+
+#--- RESULTS ---
+
+our $SQL_RESULT_STORE = "
+INSERT INTO blast_result%s ( object, ticket )
+VALUES ( ? , ? )";
+
+our $SQL_RESULT_UPDATE = "
+UPDATE blast_result%s
+SET object = ?,
+ ticket = ?
+WHERE result_id = ?";
+
+our $SQL_RESULT_RETRIEVE = "
+SELECT object
+FROM blast_result%s
+WHERE result_id = ? ";
+
+#--- HITS ---
+
+our $SQL_HIT_STORE = "
+INSERT INTO blast_hit%s ( object, ticket )
+VALUES ( ? , ? )";
+
+our $SQL_HIT_UPDATE = "
+UPDATE blast_hit%s
+SET object = ?,
+ ticket = ?
+WHERE hit_id = ?";
+
+our $SQL_HIT_RETRIEVE = "
+SELECT object
+FROM blast_hit%s
+WHERE hit_id = ? ";
+
+#--- HSPS ---
+
+our $SQL_HSP_STORE = "
+INSERT INTO blast_hsp%s ( object, ticket, chr_name, chr_start, chr_end )
+VALUES ( ? , ? , ? , ? , ? )";
+
+our $SQL_HSP_UPDATE = "
+UPDATE blast_hsp%s
+SET object = ?,
+ ticket = ?,
+ chr_name = ?,
+ chr_start = ?,
+ chr_end = ?
+WHERE hsp_id = ?";
+
+our $SQL_HSP_RETRIEVE = "
+SELECT object
+FROM blast_hsp%s
+WHERE hsp_id = ? ";
+
+
#----------------------------------------------------------------------
=head2 new
@@ -35,6 +195,413 @@ sub new {
return $self;
}
+#----------------------------------------------------------------------
+
+=head2 store
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub store {
+ my $self = shift;
+ my $obj = shift;
+ my $ret;
+ if( $obj->isa("Bio::Tools::Run::SearchMulti") ){
+ $ret = $self->store_search_multi( $obj, @_ );
+ }
+ elsif( $obj->isa("Bio::Search::Result::ResultI") ){
+ $ret = $self->store_result( $obj, @_ );
+ }
+ elsif( $obj->isa("Bio::Search::Hit::HitI") ){
+ $ret =$self->store_hit( $obj, @_ );
+ }
+ elsif( $obj->isa("Bio::Search::HSP::HSPI") ){
+ $ret = $self->store_hsp( $obj, @_ );
+ }
+ else{
+ $self->throw( "Do not know how to store objects of type ".ref($obj) );
+ }
+ return $ret;
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub retrieve {
+ my $self = shift;
+ my $caller = shift;
+ if( $caller->isa("Bio::Tools::Run::EnsemblSearchMulti") ){
+ return $self->retrieve_search_multi( @_ );
+ }
+ elsif( $caller->isa("Bio::Search::Result::ResultI") ){
+ return $self->retrieve_result( @_ );
+ }
+ elsif( $caller->isa("Bio::Search::Hit::HitI") ){
+ return $self->retrieve_hit( @_ );
+ }
+ elsif( $caller->isa("Bio::Search::HSP::HSPI") ){
+ return $self->retrieve_hsp( @_ );
+ }
+ $self->throw( "Do not know how to retrieve objects of type ".
+ ref($caller)? ref($caller) : $caller );
+}
+
+#----------------------------------------------------------------------
+
+=head2 remove
+
+ Arg [1] :
+ Function : TODO: implement remove functions
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub remove {
+ my $self = shift;
+ my $obj = shift;
+ if( $obj->isa("Bio::Tools::Run::EnsemblSearchMulti") ){
+ #return $self->remove_search_multi( @_ );
+ }
+ elsif( $obj->isa("Bio::Search::Result::ResultI") ){
+ #return $self->remove_result( @_ );
+ }
+ elsif( $obj->isa("Bio::Search::Hit::HitI") ){
+ #return $self->remove_hit( @_ );
+ }
+ elsif( $obj->isa("Bio::Search::HSP::HSPI") ){
+ #return $self->remove_hsp( @_ );
+ }
+ $self->throw( "Do not know how to remove objects of type ".
+ ref($obj) );
+}
+#----------------------------------------------------------------------
+=head2 store_search_multi
+
+ Arg [1] : Bio::Tools::Run::EnsemblSearchMulti obj
+ Function : Stores the ensembl SearchMulti container object in the database
+ Returntype: scalar (token)
+ Exceptions:
+ Caller :
+ Example : my $container_token = $blast_adpt->store_ticket( $container );
+
+=cut
+
+sub store_search_multi{
+ my $self = shift;
+ my $search_multi = shift ||
+ $self->throw( "Need a Bio::Tools::Run::EnsemblSearchMulti obj" );
+
+ my $frozen = shift || $search_multi->serialise;
+
+ my $dbh = $self->db->db_handle;
+
+ my $ticket = $search_multi->token ||
+ $self->throw( "Bio::Tools::Run::EnsemblSearchMulti obj has no ticket" );
+
+ my $sth = $dbh->prepare( $SQL_SEARCH_MULTI_RETRIEVE );
+ my $rv = $sth->execute( $ticket ) || $self->throw( $sth->errstr );
+ $sth->finish;
+
+ if( $rv < 1 ){ # Insert (do first to minimise risk of race)
+ my $sth = $dbh->prepare( $SQL_SEARCH_MULTI_STORE );
+ $sth->execute( $frozen, $ticket ) || $self->throw( $sth->errstr );
+ #$search_multi->token( $self->dbh->{mysql_insertid} );
+ $sth->finish;
+ }
+ else{ # Update
+ my $sth = $dbh->prepare( $SQL_SEARCH_MULTI_UPDATE );
+ $sth->execute( $frozen, $ticket ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ return $search_multi->token();
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve_search_multi
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub retrieve_search_multi {
+ my $self = shift;
+ my $ticket = shift || $self->throw( "Need an EnsemblSearchMulti ticket" );
+
+ my $dbh = $self->db->db_handle;
+ my $sth = $dbh->prepare( $SQL_SEARCH_MULTI_RETRIEVE );
+ my $rv = $sth->execute( $ticket ) || $self->throw( $sth->errstr );
+ if( $rv < 1 ){ $self->throw( "Token $ticket not found" ) }
+ my ( $frozen ) = $sth->fetchrow_array;
+ $frozen || $self->throw( "Object from ticket $ticket is empty" );
+ $sth->finish;
+ return $frozen;
+}
+
+
+
+#----------------------------------------------------------------------
+=head2 store_result
+
+ Arg [1] : Bio::Search::Result::EnsemblResult obj
+ Function : Stores the ensembl Result in the database
+ Returntype: scalar (token)
+ Exceptions:
+ Caller :
+ Example : my $result_token = $blast_adpt->store_result( $result );
+
+=cut
+
+sub store_result{
+ my $self = shift;
+ my $res = shift ||
+ $self->throw( "Need a Bio::Search::Result::EnsemblResult obj" );
+ my $frozen = shift || $res->serialised;
+
+ my $dbh = $self->db->db_handle;
+
+ my $ticket = $res->group_ticket;
+ my ( $id, $use_date ) = split( '!!', $res->token || '' );
+ $use_date ||= $self->use_date('RESULT');
+
+ my $rv = 0;
+ 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 $use_date = $res->use_date() ||
+ $res->use_date($self->use_date('RESULT'));
+ my $sth = $dbh->prepare( sprintf $SQL_RESULT_STORE, $use_date );
+ $sth->execute( $frozen, $ticket ) || $self->throw( $sth->errstr );
+ my $id = $dbh->{mysql_insertid};
+ $res->token( join( '!!', $id, $use_date ) );
+ $sth->finish;
+ }
+ else{ # Update
+ my $sth = $dbh->prepare( sprintf $SQL_RESULT_UPDATE, $use_date );
+ $sth->execute( $frozen, $ticket, $id ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ return $res->token();
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve_result
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub retrieve_result{
+ my $self = shift;
+ 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( 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;
+ $frozen || $self->throw( "Object from result $id is empty" );
+ $sth->finish;
+ return $frozen;
+}
+
+#----------------------------------------------------------------------
+=head2 store_hit
+
+ Arg [1] : Bio::Search::Hit::EnsemblHit obj
+ Function : Stores the ensembl Hit in the database
+ Returntype: scalar (token)
+ Exceptions:
+ Caller :
+ Example : my $hit_token = $blast_adpt->store_hit( $hit );
+
+=cut
+
+sub store_hit{
+ my $self = shift;
+ my $hit = shift ||
+ $self->throw( "Need a Bio::Search::Hit::EnsemblHit obj" );
+ my $frozen = shift || $hit->serialise;
+
+ my $dbh = $self->db->db_handle;
+
+ my $ticket = $hit->group_ticket;
+ my ( $id, $use_date ) = split( '!!', $hit->token || '' );
+ $use_date ||= '';
+
+ my $rv = 0;
+ if( $id ){
+ my $sth = $dbh->prepare( sprintf $SQL_HIT_RETRIEVE, $use_date );
+ $rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ if( $rv < 1 ){ # Insert
+ my $use_date = $hit->use_date() || $hit->use_date($self->use_date('HIT'));
+ my $sth = $dbh->prepare( sprintf $SQL_HIT_STORE, $use_date );
+ $sth->execute( $frozen, $ticket ) || $self->throw( $sth->errstr );
+ my $id = $dbh->{mysql_insertid};
+ $hit->token( join( '!!', $id, $use_date ) );
+ $sth->finish;
+ }
+ else{ # Update
+ my $sth = $dbh->prepare( sprintf $SQL_HIT_UPDATE, $use_date );
+ $sth->execute( $frozen, $ticket, $id ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ return $hit->token();
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve_hit
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub retrieve_hit{
+ my $self = shift;
+ 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( sprintf $SQL_HIT_RETRIEVE, $use_date );
+ my $rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
+ if( $rv < 1 ){ $self->throw( "Token $token not found" ) }
+ my ( $frozen ) = $sth->fetchrow_array;
+ $frozen || $self->throw( "Object from hit $id is empty" );
+ $sth->finish;
+ return $frozen;
+}
+
+#----------------------------------------------------------------------
+=head2 store_hsp
+
+ Arg [1] : Bio::Search::HSP::EnsemblHSP obj
+ Function : Stores the ensembl HSP in the database
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub store_hsp{
+ my $self = shift;
+ my $hsp = shift ||
+ $self->throw( "Need a Bio::Search::HSP::EnsemblHSP obj" );
+ my $frozen = shift || $hsp->serialise;
+
+ my $dbh = $self->db->db_handle;
+
+ my $ticket = $hsp->group_ticket;
+ my ( $id, $use_date ) = split( '!!', $hsp->token || '');
+ $use_date ||= $self->use_date('HSP');
+
+ my $chr_name = 'NULL';
+ my $chr_start = 'NULL';
+ my $chr_end = 'NULL';
+ if( my $genomic = $hsp->genomic_hit ){
+ $chr_name = $genomic->seq_id;
+ $chr_start = $genomic->start;
+ $chr_end = $genomic->end;
+ }
+
+ my $rv = 0;
+ if( $id ){
+ my $sth = $dbh->prepare( sprintf $SQL_HSP_RETRIEVE, $use_date );
+ $rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ if( $rv < 1 ){ # Insert
+ my $use_date = $hsp->use_date() || $hsp->use_date($self->use_date('HSP'));
+ my $sth = $dbh->prepare( sprintf $SQL_HSP_STORE, $use_date );
+ my @bound = ( $frozen, $ticket, $chr_name, $chr_start, $chr_end );
+ $sth->execute( @bound ) || $self->throw( $sth->errstr );
+ my $id = $dbh->{mysql_insertid};
+ $hsp->token( join( '!!', $id, $use_date ) );
+ $sth->finish;
+ }
+ else{ # Update
+ my $sth = $dbh->prepare( sprintf $SQL_HSP_UPDATE, $use_date );
+ my @bound = ( $frozen, $ticket, $chr_name, $chr_start, $chr_end, $id );
+ $sth->execute( @bound ) || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ return $hsp->token();
+}
+
+#----------------------------------------------------------------------
+
+=head2 retrieve_hsp
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub retrieve_hsp{
+ my $self = shift;
+ my $token = shift || $self->throw( "Need an HSP token" );
+ my ( $id, $use_date ) = split( '!!',$token);
+ $use_date ||= '';
+
+ my $dbh = $self->db->db_handle;
+ my $sth = $dbh->prepare( sprintf $SQL_HSP_RETRIEVE, $use_date );
+ my $rv = $sth->execute( $id ) || $self->throw( $sth->errstr );
+ if( $rv < 1 ){ $self->throw( "Token $token not found" ) }
+ my ( $frozen ) = $sth->fetchrow_array;
+ $frozen || $self->throw( "Object from hsp $id is empty" );
+ $sth->finish;
+ return $frozen;
+}
+
+
#----------------------------------------------------------------------
=head2 get_all_HSPs
@@ -54,11 +621,13 @@ sub get_all_HSPs {
my $chr_name = shift || undef;
my $chr_start = shift || undef;
my $chr_end = shift || undef;
+ my ( $id, $use_date ) = split( '!!', $ticket );
+ $use_date ||= '';
my $SQL = qq(
SELECT object
-FROM blast_hsp
-WHERE ticket = ? );
+FROM blast_hsp%s
+WHERE \(ticket = ? OR ticket = ?\) );
my $CHR_SQL = qq(
AND chr_name = ? );
@@ -67,8 +636,8 @@ AND chr_name = ? );
AND chr_start <= ?
AND chr_end >= ? );
- my $q = $SQL;
- my @binded = ( $ticket );
+ my $q = sprintf( $SQL, $use_date );
+ my @binded = ( $id, substr($id,6) );
if( $chr_name ){
$q .= $CHR_SQL;
@@ -79,12 +648,13 @@ AND chr_end >= ? );
push @binded, $chr_end, $chr_start;
}
}
- warn( "$q: ", join( ', ',@binded ) );
+# warn( "$q: ", join( ', ',@binded ) );
my $sth = $self->db->db_handle->prepare($q);
my $rv = $sth->execute( @binded ) || $self->throw( $sth->errstr );
my @hsps = map{ thaw( $_->[0] ) } @{$sth->fetchall_arrayref()};
+ $sth->finish;
return [@hsps];
}
@@ -107,12 +677,301 @@ AND chr_end >= ? );
sub get_all_SearchFeatures {
my $self = shift;
my $hsps = $self->get_all_HSPs(@_);
+ $self->dynamic_use( ref($hsps->[0] ) );
my @feats = grep{ $_ } map{ $_->ens_genomic_align } @$hsps;
return [ @feats ];
}
+sub dynamic_use {
+ my( $self, $classname ) = @_;
+ my( $parent_namespace, $module ) = $classname =~/^(.*::)(.*?)$/;
+ no strict 'refs';
+ return 1 if $parent_namespace->{$module.'::'}; # return if already used
+ eval "require $classname";
+ if($@) {
+ warn "DrawableContainer: failed to use $classname\nDrawableContainer: $@";
+ return 0;
+ }
+ $classname->import();
+ return 1;
+}
+
+#----------------------------------------------------------------------
+
+=head2 use_date
+
+ Arg [1] :
+ Function :
+ Returntype:
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+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 (Result, Hit or HSP)" );
+
+ $self->{$key} ||= {};
+ if( ! $self->{$key}->{$type} ){
+ my $sth = $self->db->db_handle->prepare( $SQL_SELECT_TABLE_LOG_CURRENT );
+ my $rv = $sth->execute( $type ) || ( warn( $sth->errstr ) && return );
+ $rv > 0 || ( warn( "No current $type table found" ) && return );
+ my $date = $sth->fetchrow_arrayref->[0];
+ $date =~ s/-//g;
+ $self->{$key}->{$type} = $date;
+ }
+ return $self->{$key}->{$type};
+}
+
+
+
+#----------------------------------------------------------------------
+
+=head2 clean_blast_database
+
+ Arg [1] : int $days
+ Function : Removes blast tickets older than $days days
+ Returntype:
+ Exceptions: SQL errors
+ Caller :
+ Example : $ba->clean_blast_database(14)
+
+=cut
+
+sub clean_blast_database{
+ my $self = shift;
+ my $days = shift || $self->throw( "Missing arg: number of days" );
+ $days =~ /\D/ && $self->throw( "Bad arg: number of days $days not int" );
+ my $dbh = $self->db->db_handle;
+
+ # Get list of tickets > $days days old
+ my $q = qq/
+SELECT ticket
+FROM blast_ticket
+WHERE update_time < SUBDATE( NOW(), INTERVAL $days DAY ) /;
+
+ my $sth = $self->db->db_handle->prepare($q);
+ my $rv = $sth->execute() || $self->throw( $sth->errstr );
+ my $res = $sth->fetchall_arrayref;
+ $sth->finish;
+
+ # Delete result and ticket rows associated with old tickets
+# my $q_del_tmpl = qq/
+#DELETE
+#FROM blast_%s
+#WHERE ticket like "%s" /;
+#
+# my @types = ( 'result','ticket' );
+# my %num_deleted = map{ $_=>0 } @types;
+#
+# foreach my $row( @$res ){
+# my $ticket = $row->[0];
+#
+# foreach my $type( @types ){
+# my $q_del = sprintf( $q_del_tmpl, $type, $ticket );
+# my $sth = $self->db->db_handle->prepare($q_del);
+# my $rv = $sth->execute() || $self->throw( $sth->errstr );
+# $num_deleted{$type} += $rv;
+# }
+# }
+# map{ warn("Purging $days days: Deleted $num_deleted{$_} rows of type $_\n") }
+# keys %num_deleted;
+
+ # Drop daily Result, Hit and HSP tables not updated within $days days
+ my $q_find = 'show table status like ?';
+ my $sth2 = $dbh->prepare( $q_find );
+ $sth2->execute( "blast_result%" ) || $self->throw( $sth2->errstr );
+ my $res_res = $sth2->fetchall_arrayref();
+ $sth2->execute( "blast_hit%" ) || $self->throw( $sth2->errstr );
+ my $hit_res = $sth2->fetchall_arrayref();
+ $sth2->execute( "blast_hsp%" ) || $self->throw( $sth2->errstr );
+ my $hsp_res = $sth2->fetchall_arrayref();
+
+ my @deletable_hit_tables;
+ foreach my $row( @$res_res, @$hit_res, @$hsp_res ){
+ my $table_name = $row->[0];
+ my $num_rows = $row->[3];
+ my $update_time = $row->[11]; # Should be a string like 2003-08-15 10:36:56
+ my @time = split( /[-:\s]/, $update_time );
+
+ my $epoch_then = timelocal( $time[5], $time[4], $time[3],
+ $time[2], $time[1]-1, $time[0] - 1900 );
+ my $secs_old = time() - $epoch_then;
+ my $days_old = $secs_old / ( 60 * 60 * 24 );
+ if( $days_old > $days ){
+ warn( "Dropping table $table_name: $num_rows rows\n" );
+ my $sth_drop = $dbh->prepare( "DROP table $table_name" );
+ my $sth_log = $dbh->prepare( $SQL_TABLE_LOG_UPDATE );
+ $sth_drop->execute || $self->throw( $sth_drop->errstr );
+ my( $se,$mi,$hr,$da,$mo,$yr ) = (localtime)[0,1,2,3,4,5];
+ my $now = sprintf( "%4d-%2d-%2d %2d:%2d:%2d",
+ $yr+1900,$mo+1,$da,$hr,$mi,$se );
+ $sth_log->execute
+ ('DELETED',$now,$num_rows,$table_name) ||
+ $self->throw( $sth_log->errstr );
+ }
+ }
+
+
+ return 1;
+}
+
+#----------------------------------------------------------------------
+
+=head2 create_tables
+ Arg [1] : none
+ 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
+ Exceptions:
+ Caller :
+ Example :
+=cut
+
+sub create_tables {
+ my $self = shift;
+ my $dbh = $self->db->db_handle;
+
+ # Get list of existing tables in database
+ my $q = 'show tables like ?';
+ my $sth = $dbh->prepare( $q );
+ my $rv_tck = $sth->execute("blast_ticket") || $self->throw($sth->errstr);
+ my $rv_log = $sth->execute("blast_table_log" )|| $self->throw($sth->errstr);
+ $sth->finish;
+
+ if( $rv_tck == 0 ){
+ warn( "Creating blast_ticket table\n" );
+ my $sth = $dbh->prepare( $SQL_CREATE_TICKET );
+ my $rv = $sth->execute() || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ else{ warn( "blast_ticket table already exists\n" ) }
+
+ if( $rv_log == 0 ){
+ warn( "Creating blast_result table\n" );
+ my $sth = $dbh->prepare( $SQL_CREATE_TABLE_LOG );
+ my $rv = $sth->execute() || $self->throw( $sth->errstr );
+ $sth->finish;
+ }
+ else{ warn( "blast_table_log table already exists\n" ) }
+
+ return 1;
+}
+
+#----------------------------------------------------------------------
+
+=head2 rotate_daily_tables
+
+ Arg [1] : none
+ 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.
+ Returntype: boolean
+ Exceptions:
+ Caller :
+ Example :
+
+=cut
+
+sub rotate_daily_tables {
+ my $self = shift;
+ my $dbh = $self->db->db_handle;
+
+ # Get date
+ 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";
+
+ # Get list of existing tables in database
+ 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);
+ $sth->finish;
+
+ 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 $sth1 = $dbh->prepare( $q );
+ my $rv = $sth1->execute() || $self->throw( $sth1->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 ) );
+ $sth1->finish();
+ $sth2->finish();
+ $sth3->finish();
+ }
+ else{ warn( "Today's $res_table table already exists\n" ) }
+
+ if( $rv_hit == 0 ){
+ warn( "Creating today's $hit_table table\n" );
+
+ # Create new table
+ my $q = sprintf($SQL_CREATE_DAILY_HIT, $hit_table);
+ my $sth1 = $dbh->prepare( $q );
+ my $rv = $sth1->execute() || $self->throw( $sth1->errstr );
+
+ # Flip current table in blast_table_tog
+ my $last_date = $self->use_date( "HIT" ) || '';
+ my $sth2 = $dbh->prepare( $SQL_TABLE_LOG_INSERT );
+ my $sth3 = $dbh->prepare( $SQL_TABLE_LOG_UPDATE );
+ $sth2->execute( "$hit_table",'CURRENT','HIT',$date )
+ || die( $self->throw( $sth2->errstr ) );
+ $sth3->execute( 'FILLED','0',0,"blast_hit$last_date")
+ || die( $self->throw( $sth3->errstr ) );
+ $sth1->finish();
+ $sth2->finish();
+ $sth3->finish();
+ }
+ else{ warn( "Today's $hit_table table already exists\n" ) }
+
+ if( $rv_hsp == 0 ){
+ warn( "Creating today's $hsp_table table\n" );
+
+ # Create new table
+ my $q = sprintf($SQL_CREATE_DAILY_HSP, $hsp_table );
+ my $sth1 = $dbh->prepare( $q );
+ my $rv = $sth1->execute() || $self->throw( $sth1->errstr );
+
+ # Flip current table in blast_table_tog
+ my $last_date = $self->use_date( "HSP" ) || '';
+ my $sth2 = $dbh->prepare( $SQL_TABLE_LOG_INSERT );
+ my $sth3 = $dbh->prepare( $SQL_TABLE_LOG_UPDATE );
+ $sth2->execute( "$hsp_table",'CURRENT','HSP',$date )
+ || die( $self->throw( $sth2->errstr ) );
+ $sth3->execute( 'FILLED','0',0,"blast_hsp$last_date")
+ || die( $self->throw( $sth3->errstr ) );
+ $sth1->finish();
+ $sth2->finish();
+ $sth3->finish();
+ }
+ else{ warn( "Today's $hsp_table table already exists\n" ) }
+ return 1;
+}
#----------------------------------------------------------------------
1;