From 6e515886137444d925b95f805a469a61b4abf2af Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Thu, 3 Oct 2013 12:45:51 +0100
Subject: [PATCH] drop fetch_all_by_from_analysis_id_and_branch_code() method
and rely on AUTOLOADed BaseAdaptor's methods instead
---
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 10 ++++---
.../EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 7 +++--
.../EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm | 26 -------------------
3 files changed, 11 insertions(+), 32 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 90ec28047..32a4c9d93 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -164,11 +164,13 @@ sub dataflow_rules { # if ever set will prevent the Job from fetching rules f
my $branch_code = Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code($branch_name_or_code);
- $self->{'_dataflow_rules'}{$branch_code} = shift if(@_);
+ if(@_) {
+ $self->{'_dataflow_rules'}{$branch_code} = shift @_;
+ }
+
+ $self->{'_dataflow_rules'} ||= $self->adaptor->db->get_DataflowRuleAdaptor->fetch_all_by_from_analysis_id_HASHED_FROM_branch_code( $self->analysis_id );
- return $self->{'_dataflow_rules'}
- ? ( $self->{'_dataflow_rules'}{$branch_code} || [] )
- : $self->adaptor->db->get_DataflowRuleAdaptor->fetch_all_by_from_analysis_id_and_branch_code($self->analysis_id, $branch_code);
+ return $self->{'_dataflow_rules'}{$branch_code} || [];
}
sub stdout_file {
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index 2d4b3b420..217998c17 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -48,6 +48,7 @@ use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Hive::AnalysisJob;
+use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
@@ -553,8 +554,10 @@ sub release_and_age_job {
sub gc_dataflow {
my ($self, $analysis, $job_id, $branch_name) = @_;
- unless(@{ $self->db->get_DataflowRuleAdaptor->fetch_all_by_from_analysis_id_and_branch_code($analysis->dbID, $branch_name) }) {
- return 0; # no corresponding gc_dataflow rule has been defined
+ my $branch_code = Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code($branch_name);
+
+ unless( $self->db->get_DataflowRuleAdaptor->count_all_by_from_analysis_id_AND_branch_code($analysis->dbID, $branch_code) ) {
+ return 0; # just return if no corresponding gc_dataflow rule has been defined
}
my $job = $self->fetch_by_dbID($job_id);
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
index 21410642e..900e47751 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
@@ -84,31 +84,5 @@ sub branch_name_2_code {
return defined($branch_code) ? $branch_code : die "Could not map the branch_name '$branch_name_or_code' to the internal code";
}
-
-=head2 fetch_all_by_from_analysis_id_and_branch_code
-
- Args : unsigned int $analysis_id, unsigned int $branch_code
- Example : my @rules = @{$ruleAdaptor->fetch_all_by_from_analysis_id_and_branch_code($analysis_id, $branch_code)};
- Description: searches database for rules with given from_analysis_id and branch_code
- and returns all such rules in a list (by reference)
- Returntype : reference to list of Bio::EnsEMBL::Hive::DataflowRule objects
- Exceptions : none
- Caller : Bio::EnsEMBL::Hive::AnalysisJob::dataflow_output_id
-
-=cut
-
-sub fetch_all_by_from_analysis_id_and_branch_code {
- my ($self, $analysis_id, $branch_name_or_code) = @_;
-
- return [] unless($analysis_id);
-
- my $branch_code = $self->branch_name_2_code($branch_name_or_code);
-
- my $constraint = "from_analysis_id=${analysis_id} AND branch_code=${branch_code}";
-
- return $self->fetch_all($constraint);
-}
-
-
1;
--
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