From 09e3c9b8b73e7638fa12fdbd9ef5adc6145dccee Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Mon, 22 Sep 2014 16:13:26 +0100
Subject: [PATCH] API change: Q::print_analysis_status now takes an obligatory
$list_of_analyses
---
modules/Bio/EnsEMBL/Hive/Queen.pm | 15 ++++++++++++---
scripts/beekeeper.pl | 9 ++++-----
2 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Queen.pm b/modules/Bio/EnsEMBL/Hive/Queen.pm
index d11dc16de..c48a53dbc 100644
--- a/modules/Bio/EnsEMBL/Hive/Queen.pm
+++ b/modules/Bio/EnsEMBL/Hive/Queen.pm
@@ -700,10 +700,19 @@ sub get_remaining_jobs_show_hive_progress {
}
+=head2 print_analysis_status
+
+ Arg [1] : $list_of_analyses
+ Example : $queen->print_analysis_status( [ $analysis_A, $analysis_B ] );
+ Description: Runs through all analyses in the given list and prints their stats.
+ Exceptions : none
+ Caller : beekeeper.pl
+
+=cut
+
sub print_analysis_status {
- my ($self, $filter_analysis) = @_;
+ my ($self, $list_of_analyses) = @_;
- my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
print $analysis->stats->toString . "\n";
}
@@ -715,7 +724,7 @@ sub print_analysis_status {
Example : $queen->register_all_workers_dead();
Description: Registers all workers dead
Exceptions : none
- Caller : beekeepers and other external processes
+ Caller : beekeeper.pl
=cut
diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl
index 2ec52cb4d..6bea0fba9 100755
--- a/scripts/beekeeper.pl
+++ b/scripts/beekeeper.pl
@@ -253,7 +253,7 @@ sub main {
if ($max_loops) { # positive $max_loop means limited, negative means unlimited
- run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $analysis, $run_job_id, $force);
+ run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $analysis, $run_job_id, $force);
} else {
# the output of several methods will look differently depending on $analysis being [un]defined
@@ -261,7 +261,7 @@ sub main {
if($sync) {
$queen->synchronize_hive( $list_of_analyses );
}
- $queen->print_analysis_status($analysis) unless($self->{'no_analysis_stats'});
+ $queen->print_analysis_status( $list_of_analyses ) unless($self->{'no_analysis_stats'});
if($show_worker_stats) {
print "\n===== List of live Workers according to the Queen: ======\n";
@@ -326,10 +326,9 @@ sub generate_worker_cmd {
}
sub run_autonomously {
- my ($self, $max_loops, $keep_alive, $queen, $valley, $run_analysis, $run_job_id, $force) = @_;
+ my ($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $run_analysis, $run_job_id, $force) = @_;
my $resourceless_worker_cmd = generate_worker_cmd($self, $run_analysis, $run_job_id, $force);
- my $special_task = $run_analysis || $run_job_id;
my $rc_id2name = $self->{'dba'}->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();
my %meadow_type_rc_name2resource_param_list = ();
@@ -353,7 +352,7 @@ sub run_autonomously {
$queen->check_for_dead_workers($valley, 0);
- $queen->print_analysis_status unless($self->{'no_analysis_stats'});
+ $queen->print_analysis_status( $list_of_analyses ) unless($self->{'no_analysis_stats'});
$self->{'dba'}->get_RoleAdaptor->print_active_role_counts;
my $workers_to_submit_by_meadow_type_rc_name
--
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