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Commit 41457f6a authored by Leo Gordon's avatar Leo Gordon
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switched Queen to become descendent of Hive::DBSQL::ObjectAdaptor and removed... 

switched Queen to become descendent of Hive::DBSQL::ObjectAdaptor and removed _generic_fetch from it
parent 81c1b1e6
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Showing with 39 additions and 177 deletions
modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
View file @ 41457f6a
......@@ -150,13 +150,16 @@ sub fetch_all {
my ($self, $constraint, $one_per_key, $key_list, $value_column) = @_;
my $table_name = $self->table_name();
my $columns_csv = join(', ', keys %{$self->column_set()});
my $sql = "SELECT $columns_csv FROM $table_name";
my $sql = 'SELECT ' . join(', ', keys %{$self->column_set()}) . " FROM $table_name";
if($constraint) {
# in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
$sql .= (($constraint=~/\bJOIN\b/i) ? ' ' : ' WHERE ') . $constraint;
if($constraint=~/\bJOIN\b/i) {
$sql = 'SELECT ' . join(', ', map { "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name $constraint";
} else {
$sql .= ' WHERE '.$constraint;
}
}
# warn "SQL: $sql\n";
......
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @ 41457f6a
......@@ -67,9 +67,23 @@ use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash'); # import 'destringify()' and 'dir_revhash()'
use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
sub default_table_name {
return 'worker';
}
sub default_insertion_method {
return 'INSERT';
}
sub object_class {
return 'Bio::EnsEMBL::Hive::Worker';
}
############################
......@@ -302,6 +316,7 @@ sub register_worker_death {
}
sub check_for_dead_workers { # scans the whole Valley for lost Workers (but ignores unreachagle ones)
my ($self, $valley, $check_buried_in_haste) = @_;
......@@ -425,38 +440,37 @@ sub reset_job_by_dbID_and_sync {
#
######################################
# Note: asking for Queen->fetch_overdue_workers(0) essentially means
# "fetch all workers known to the Queen not to be officially dead"
#
sub fetch_overdue_workers {
my ($self,$overdue_secs) = @_;
my ($self,$overdue_secs) = @_;
$overdue_secs = 3600 unless(defined($overdue_secs));
$overdue_secs = 3600 unless(defined($overdue_secs));
my $constraint = "w.cause_of_death='' AND ".
my $constraint = "cause_of_death='' AND ".
( ($self->dbc->driver eq 'sqlite')
? "(strftime('%s','now')-strftime('%s',w.last_check_in))>$overdue_secs"
: "(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(w.last_check_in))>$overdue_secs");
return $self->_generic_fetch($constraint);
? "(strftime('%s','now')-strftime('%s',last_check_in))>$overdue_secs"
: "(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(last_check_in))>$overdue_secs");
return $self->fetch_all( $constraint );
}
sub fetch_failed_workers {
my $self = shift;
my $self = shift;
my $constraint = "w.cause_of_death='FATALITY' ";
return $self->_generic_fetch($constraint);
return $self->fetch_all( "cause_of_death='FATALITY'" );
}
sub fetch_all_dead_workers_with_jobs {
my $self = shift;
# SELECT w.* FROM worker h, job j WHERE w.worker_id=j.worker_id AND w.cause_of_death!='' AND j.status NOT IN ('DONE', 'READY','FAILED', 'PASSED_ON') GROUP BY w.worker_id
sub fetch_all_dead_workers_with_jobs {
my $self = shift;
my $constraint = "w.cause_of_death!='' ";
my $join = [[['job', 'j'], " w.worker_id=j.worker_id AND j.status NOT IN ('DONE', 'READY', 'FAILED', 'PASSED_ON') GROUP BY w.worker_id"]];
return $self->_generic_fetch($constraint, $join);
return $self->fetch_all( "JOIN job j USING(worker_id) WHERE j.status NOT IN ('DONE', 'READY', 'FAILED', 'PASSED_ON') GROUP BY worker_id" );
}
=head2 synchronize_hive
Arg [1] : $filter_analysis (optional)
......@@ -865,6 +879,7 @@ sub print_running_worker_counts {
printf("%30s : %d workers\n\n", '======= TOTAL =======', $total_workers);
}
=head2 monitor
Arg[1] : --none--
......@@ -898,6 +913,7 @@ sub monitor {
$sth->execute();
}
=head2 register_all_workers_dead
Example : $queen->register_all_workers_dead();
......@@ -918,11 +934,6 @@ sub register_all_workers_dead {
}
#
# INTERNAL METHODS
#
###################
sub _pick_best_analysis_for_new_worker {
my $self = shift;
my $rc_id = shift; # this parameter will need to percolate very deep
......@@ -958,156 +969,4 @@ sub _pick_best_analysis_for_new_worker {
}
=head2 fetch_by_dbID
Arg [1] : int $id
the unique database identifier for the feature to be obtained
Example : $feat = $queen->fetch_by_dbID(1234);
Description: Returns the feature created from the database defined by the
the id $id.
Returntype : Bio::EnsEMBL::Hive::Worker
Exceptions : thrown if $worker_id is not defined
Caller : general
=cut
sub fetch_by_dbID {
my ($self, $worker_id) = @_;
unless(defined $worker_id) {
throw("fetch_by_dbID must have an id");
}
my ($obj) = @{$self->_generic_fetch( "w.worker_id = $worker_id" ) };
return $obj;
}
=head2 _generic_fetch
Arg [1] : (optional) string $constraint
An SQL query constraint (i.e. part of the WHERE clause)
Arg [2] : (optional) string $logic_name
the logic_name of the analysis of the features to obtain
Example : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
Description: Performs a database fetch and returns feature objects in
contig coordinates.
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : none
Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch
=cut
sub _generic_fetch {
my ($self, $constraint, $join) = @_;
my @tables = $self->_tables;
my $columns = join(', ', $self->_columns());
if ($join) {
foreach my $single_join (@{$join}) {
my ($tablename, $condition, $extra_columns) = @{$single_join};
if ($tablename && $condition) {
push @tables, $tablename;
if($constraint) {
$constraint .= " AND $condition";
} else {
$constraint = " $condition";
}
}
if ($extra_columns) {
$columns .= ", " . join(', ', @{$extra_columns});
}
}
}
#construct a nice table string like 'table1 t1, table2 t2'
my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
my $sql = "SELECT $columns FROM $tablenames";
my $default_where = $self->_default_where_clause;
my $final_clause = $self->_final_clause;
#append a where clause if it was defined
if($constraint) {
$sql .= " WHERE $constraint ";
if($default_where) {
$sql .= " AND $default_where ";
}
} elsif($default_where) {
$sql .= " WHERE $default_where ";
}
#append additional clauses which may have been defined
$sql .= " $final_clause";
my $sth = $self->prepare($sql);
$sth->execute;
# print STDERR $sql,"\n";
return $self->_objs_from_sth($sth);
}
sub _tables {
my $self = shift;
return (['worker', 'w']);
}
sub _columns {
my $self = shift;
return qw (w.worker_id
w.analysis_id
w.meadow_type
w.meadow_name
w.host
w.process_id
w.work_done
w.status
w.born
w.last_check_in
w.died
w.cause_of_death
w.log_dir
);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my %column;
$sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
my @workers = ();
while ($sth->fetch()) {
my $worker = Bio::EnsEMBL::Hive::Worker->new(
-adaptor => $self,
-dbID => $column{'worker_id'},
-analysis_id => $column{'analysis_id'},
-meadow_type => $column{'meadow_type'},
-meadow_name => $column{'meadow_name'},
-host => $column{'host'},
-process_id => $column{'process_id'},
-work_done => $column{'work_done'},
-status => $column{'status'},
-born => $column{'born'},
-last_check_in => $column{'last_check_in'},
-died => $column{'died'},
-cause_of_death => $column{'cause_of_death'},
-log_dir => $column{'log_dir'},
);
push @workers, $worker;
}
$sth->finish;
return \@workers
}
1;
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