From 743d8d55b645cb64b4202402db84d653d26db306 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 23 Sep 2014 19:19:15 +0100
Subject: [PATCH] API change : AJA::fetch_all_by_analysis_id_status now takes
an optional $list_of_analyses argument
---
.../Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 16 ++++++++++++----
scripts/beekeeper.pl | 2 +-
2 files changed, 13 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index b751244f8..7b34d1073 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -138,21 +138,29 @@ sub store_jobs_and_adjust_counters {
=head2 fetch_all_by_analysis_id_status
- Arg [1] : (optional) int $analysis_id
+ Arg [1] : (optional) listref $list_of_analyses
Arg [2] : (optional) string $status
Arg [3] : (optional) int $retry_at_least
Example : $all_failed_jobs = $adaptor->fetch_all_by_analysis_id_status(undef, 'FAILED');
- $analysis_done_jobs = $adaptor->fetch_all_by_analysis_id_status($analysis->dbID, 'DONE');
+ $analysis_done_jobs = $adaptor->fetch_all_by_analysis_id_status( $list_of_analyses, 'DONE');
Description: Returns a list of all jobs filtered by given analysis_id (if specified) and given status (if specified).
Returntype : reference to list of Bio::EnsEMBL::Hive::AnalysisJob objects
=cut
sub fetch_all_by_analysis_id_status {
- my ($self, $analysis_id, $status, $retry_count_at_least) = @_;
+ my ($self, $list_of_analyses, $status, $retry_count_at_least) = @_;
my @constraints = ();
- push @constraints, "analysis_id=$analysis_id" if ($analysis_id);
+
+ if($list_of_analyses) {
+ if(ref($list_of_analyses) eq 'ARRAY') {
+ push @constraints, "analysis_id IN (".(join(',', map {$_->dbID} @$list_of_analyses)).")";
+ } else {
+ push @constraints, "analysis_id=$list_of_analyses"; # for compatibility with old interface
+ }
+ }
+
push @constraints, "status='$status'" if ($status);
push @constraints, "retry_count >= $retry_count_at_least" if ($retry_count_at_least);
diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl
index 4acb87d79..328f52e46 100755
--- a/scripts/beekeeper.pl
+++ b/scripts/beekeeper.pl
@@ -275,7 +275,7 @@ sub main {
if($show_failed_jobs) {
print("===== failed jobs\n");
- my $failed_job_list = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status($analysis && $analysis->dbID, 'FAILED');
+ my $failed_job_list = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status( $self->{'logic_name'} and $list_of_analyses , 'FAILED');
foreach my $job (@{$failed_job_list}) {
print $job->toString. "\n";
--
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