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Commit 9888a01d authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Readability fix in store().

parent abdb6ad5
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Showing with 59 additions and 51 deletions
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
View file @ 9888a01d
......@@ -359,46 +359,49 @@ sub store {
my $rows_inserted = 0;
my $sth;
if($analysis->created ) {
if ( $analysis->created() ) {
# we use insert IGNORE so that this method can be used in a multi-process
# environment. If another process has already written this record
# then there will not be a problem
# We use insert IGNORE so that this method can be used in a
# multi-process environment. If another process has already written
# this record then there will not be a problem.
$sth = $self->prepare( q{
$sth = $self->prepare(
q{
INSERT IGNORE INTO analysis
SET created = ?,
logic_name = ?,
db = ?,
db_version = ?,
db = ?,
db_version = ?,
db_file = ?,
program = ?,
program_version = ?,
program_file = ?,
parameters = ?,
parameters = ?,
module = ?,
module_version = ?,
gff_source = ?,
gff_feature = ?
}
);
$sth->bind_param( 1, $analysis->created, SQL_DATETIME );
$sth->bind_param( 2, $analysis->logic_name, SQL_VARCHAR );
$sth->bind_param( 3, $analysis->db, SQL_VARCHAR );
$sth->bind_param( 4, $analysis->db_version, SQL_VARCHAR );
$sth->bind_param( 5, $analysis->db_file, SQL_VARCHAR );
$sth->bind_param( 6, $analysis->program, SQL_VARCHAR );
$sth->bind_param( 7, $analysis->program_version, SQL_VARCHAR );
$sth->bind_param( 8, $analysis->program_file, SQL_VARCHAR );
$sth->bind_param( 9, $analysis->parameters, SQL_VARCHAR );
$sth->bind_param( 10, $analysis->module, SQL_VARCHAR );
$sth->bind_param( 11, $analysis->module_version, SQL_VARCHAR );
$sth->bind_param( 12, $analysis->gff_source, SQL_VARCHAR );
$sth->bind_param( 13, $analysis->gff_feature, SQL_VARCHAR );
} );
$sth->bind_param(1,$analysis->created,SQL_DATETIME);
$sth->bind_param(2,$analysis->logic_name,SQL_VARCHAR);
$sth->bind_param(3,$analysis->db,SQL_VARCHAR);
$sth->bind_param(4,$analysis->db_version,SQL_VARCHAR);
$sth->bind_param(5,$analysis->db_file,SQL_VARCHAR);
$sth->bind_param(6,$analysis->program,SQL_VARCHAR);
$sth->bind_param(7,$analysis->program_version,SQL_VARCHAR);
$sth->bind_param(8,$analysis->program_file,SQL_VARCHAR);
$sth->bind_param(9,$analysis->parameters,SQL_VARCHAR);
$sth->bind_param(10,$analysis->module,SQL_VARCHAR);
$sth->bind_param(11,$analysis->module_version,SQL_VARCHAR);
$sth->bind_param(12,$analysis->gff_source,SQL_VARCHAR);
$sth->bind_param(13,$analysis->gff_feature,SQL_VARCHAR);
$rows_inserted = $sth->execute();
} else {
$sth = $self->prepare( q{
$sth = $self->prepare(
q{
INSERT IGNORE INTO analysis
SET created = now(),
logic_name = ?,
......@@ -408,45 +411,50 @@ sub store {
program = ?,
program_version = ?,
program_file = ?,
parameters = ?,
parameters = ?,
module = ?,
module_version = ?,
gff_source = ?,
gff_feature = ?
} );
$sth->bind_param(1,$analysis->logic_name,SQL_VARCHAR);
$sth->bind_param(2,$analysis->db,SQL_VARCHAR);
$sth->bind_param(3,$analysis->db_version,SQL_VARCHAR);
$sth->bind_param(4,$analysis->db_file,SQL_VARCHAR);
$sth->bind_param(5,$analysis->program,SQL_VARCHAR);
$sth->bind_param(6,$analysis->program_version,SQL_VARCHAR);
$sth->bind_param(7,$analysis->program_file,SQL_VARCHAR);
$sth->bind_param(8,$analysis->parameters,SQL_VARCHAR);
$sth->bind_param(9,$analysis->module,SQL_VARCHAR);
$sth->bind_param(10,$analysis->module_version,SQL_VARCHAR);
$sth->bind_param(11,$analysis->gff_source,SQL_VARCHAR);
$sth->bind_param(12,$analysis->gff_feature,SQL_VARCHAR);
}
);
$sth->bind_param( 1, $analysis->logic_name, SQL_VARCHAR );
$sth->bind_param( 2, $analysis->db, SQL_VARCHAR );
$sth->bind_param( 3, $analysis->db_version, SQL_VARCHAR );
$sth->bind_param( 4, $analysis->db_file, SQL_VARCHAR );
$sth->bind_param( 5, $analysis->program, SQL_VARCHAR );
$sth->bind_param( 6, $analysis->program_version, SQL_VARCHAR );
$sth->bind_param( 7, $analysis->program_file, SQL_VARCHAR );
$sth->bind_param( 8, $analysis->parameters, SQL_VARCHAR );
$sth->bind_param( 9, $analysis->module, SQL_VARCHAR );
$sth->bind_param( 10, $analysis->module_version, SQL_VARCHAR );
$sth->bind_param( 11, $analysis->gff_source, SQL_VARCHAR );
$sth->bind_param( 12, $analysis->gff_feature, SQL_VARCHAR );
$rows_inserted = $sth->execute();
}
} ## end else [ if ( $analysis->created...)]
my $dbID;
# if we need to fetch the timestamp, or the insert failed due to existance
# of an existing entry, we need to retrieve the entry from the db
# note: $sth->execute can return 0E0 on error which is zero, but true
# which is why the $rows_inserted clause was added.
if(!$analysis->created() || !$rows_inserted || $rows_inserted == 0) {
my $new_analysis = $self->fetch_by_logic_name($analysis->logic_name);
if(!$new_analysis) {
throw("Could not retrieve just stored analysis from database.\n" .
"Possibly incorrect db permissions or missing analysis table\n");
# If we need to fetch the timestamp, or the insert failed due to
# existance of an existing entry, we need to retrieve the entry from
# the database. Note: $sth->execute() may return 0E0 on error which
# is zero, but true which is why the $rows_inserted clause was added.
if ( !$analysis->created() || !$rows_inserted || $rows_inserted == 0 )
{
my $new_analysis =
$self->fetch_by_logic_name( $analysis->logic_name );
if ( !$new_analysis ) {
throw("Could not retrieve just stored analysis from database.\n"
. "Possibly incorrect db permissions or missing analysis table\n"
);
}
$dbID = $new_analysis->dbID();
$analysis->created($new_analysis->created());
}
$analysis->created( $new_analysis->created() );
}
$dbID ||= $sth->{'mysql_insertid'};
$sth->finish();
......
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