From 17c0bd74cdb379f9b6bd618d417f956772ea40bc Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 23 Sep 2014 12:54:14 +0100
Subject: [PATCH] API change: Q::get_num_failed_analyses() takes an obligatory
$list_of_analyses and performs API level filtering (may affect speed)
---
modules/Bio/EnsEMBL/Hive/Queen.pm | 35 +++++++++++++++----------------
scripts/beekeeper.pl | 2 +-
2 files changed, 18 insertions(+), 19 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Queen.pm b/modules/Bio/EnsEMBL/Hive/Queen.pm
index 6474f27c3..65b132e14 100644
--- a/modules/Bio/EnsEMBL/Hive/Queen.pm
+++ b/modules/Bio/EnsEMBL/Hive/Queen.pm
@@ -649,12 +649,10 @@ sub check_nothing_to_run_but_semaphored { # make sure it is run after a recent
=head2 get_num_failed_analyses
- Arg [1] : Bio::EnsEMBL::Hive::AnalysisStats object (optional)
- Example : if( $self->get_num_failed_analyses( $my_analysis )) { do_something; }
- Example : my $num_failed_analyses = $self->get_num_failed_analyses();
- Description: Reports all failed analyses and returns
- either the number of total failed (if no $filter_analysis was provided)
- or 1/0, depending on whether $filter_analysis failed or not.
+ Arg [1] : $list_of_analyses
+ Example : my $num_failed_analyses = $self->get_num_failed_analyses( [ $analysis_A, $analysis_B ] );
+ Example : if( $self->get_num_failed_analyses( [ $analysis_A, $analysis_B, $analysis_C ] )) { do_something; }
+ Description: Reports all failed analyses and returns their number.
Returntype : int
Exceptions : none
Caller : beekeeper.pl
@@ -662,22 +660,23 @@ sub check_nothing_to_run_but_semaphored { # make sure it is run after a recent
=cut
sub get_num_failed_analyses {
- my ($self, $filter_analysis) = @_;
-
- my $failed_analyses = $self->db->get_AnalysisAdaptor->fetch_all_failed_analyses();
+ my ($self, $list_of_analyses) = @_;
- my $filter_analysis_failed = 0;
+ my $failed_analyses_counter = 0;
- foreach my $failed_analysis (@$failed_analyses) {
- warn "\t##########################################################\n";
- warn "\t# Too many jobs in analysis '".$failed_analysis->logic_name."' FAILED #\n";
- warn "\t##########################################################\n\n";
- if($filter_analysis and ($filter_analysis->dbID == $failed_analysis)) {
- $filter_analysis_failed = 1;
+ foreach my $analysis (@$list_of_analyses) {
+ my $stats = $analysis->stats;
+ if( $stats->status eq 'FAILED') {
+ my $logic_name = $analysis->logic_name;
+ my $failed_job_count = $stats->failed_job_count;
+ my $tolerance = $analysis->failed_job_tolerance;
+ warn "\t##################################################################################################\n";
+ warn "\t# Analysis '$logic_name' has FAILED (failed Jobs: $failed_job_count, tolerance: $tolerance\%) #\n";
+ warn "\t##################################################################################################\n";
+ $failed_analyses_counter++;
}
}
-
- return $filter_analysis ? $filter_analysis_failed : scalar(@$failed_analyses);
+ return $failed_analyses_counter;
}
diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl
index 1c42fc107..11e83775e 100755
--- a/scripts/beekeeper.pl
+++ b/scripts/beekeeper.pl
@@ -391,7 +391,7 @@ sub run_autonomously {
print "Not submitting any workers this iteration\n";
}
- $failed_analyses = $queen->get_num_failed_analyses( $run_analysis );
+ $failed_analyses = $queen->get_num_failed_analyses( $list_of_analyses );
$num_of_remaining_jobs = $queen->get_remaining_jobs_show_hive_progress( $run_analysis );
} while( $keep_alive
--
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