Commit 18417dbf authored by Leo Gordon's avatar Leo Gordon
Browse files

simplify logging of submission output/error streams

parent b2155f15
......@@ -13,6 +13,7 @@ BEGIN {
use Getopt::Long;
use File::Path 'make_path';
use Bio::EnsEMBL::Hive::Utils ('script_usage', 'destringify');
use Bio::EnsEMBL::Hive::Utils::Config;
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
......@@ -68,6 +69,7 @@ sub main {
$self->{'hive_log_dir'} = undef;
$self->{'submit_stdout_file'} = undef;
$self->{'submit_stderr_file'} = undef;
$self->{'submit_log_dir'} = undef;
GetOptions(
# connection parameters
......@@ -103,6 +105,7 @@ sub main {
'debug=i' => \$self->{'debug'},
'submit_stdout_file=s' => \$self->{'submit_stdout_file'},
'submit_stderr_file=s' => \$self->{'submit_stderr_file'},
'submit_log_dir=s' => \$self->{'submit_log_dir'},
# other commands/options
'h|help' => \$help,
......@@ -332,6 +335,11 @@ sub run_autonomously {
$meadow_type_rc_name2resource_param_list{ $rd->meadow_type() }{ $rc_id2name->{$rd->resource_class_id} } = [ $rd->submission_cmd_args, $rd->worker_cmd_args ];
}
if( $self->{'submit_log_dir'} ) {
make_path( $self->{'submit_log_dir'} );
}
my $beekeeper_pid = $$;
my $iteration=0;
my $num_of_remaining_jobs=0;
my $failed_analyses=0;
......@@ -369,6 +377,11 @@ sub run_autonomously {
. ($special_task ? '' : " -rc_name $rc_name")
. (defined($worker_cmd_args) ? " $worker_cmd_args" : '');
if( $self->{'submit_log_dir'} ) {
$self->{'submit_stdout_file'} = $self->{'submit_log_dir'} . "/submit_${beekeeper_pid}_iter${iteration}_${rc_name}.out";
$self->{'submit_stderr_file'} = $self->{'submit_log_dir'} . "/submit_${beekeeper_pid}_iter${iteration}_${rc_name}.err";
}
$this_meadow->submit_workers($specific_worker_cmd, $this_meadow_rc_worker_count, $iteration,
$rc_name, $submission_cmd_args || '',
$self->{'submit_stdout_file'}, $self->{'submit_stderr_file'});
......
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