From 1a4664d667306ff47af608e6fd14d881d10f642b Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 1 Jul 2014 12:57:45 +0100
Subject: [PATCH] internal api cleanup: switched to more intuitive
set_and_update_status/check_in_worker/check_in_job calls
---
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 10 ++++++----
.../Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 6 +++---
modules/Bio/EnsEMBL/Hive/Process.pm | 2 +-
modules/Bio/EnsEMBL/Hive/Worker.pm | 16 +++++++++++++---
4 files changed, 23 insertions(+), 11 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 8096e23c4..89d49059f 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -134,12 +134,14 @@ sub semaphored_job_id {
return $self->{'_semaphored_job_id'};
}
-
-sub update_status {
+sub set_and_update_status {
my ($self, $status ) = @_;
+
$self->status($status);
- return unless($self->adaptor);
- $self->adaptor->update_status($self);
+
+ if(my $adaptor = $self->adaptor) {
+ $adaptor->check_in_job($self);
+ }
}
sub dataflow_rules { # if ever set will prevent the Job from fetching rules from the DB
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index e85f7c549..cbfcd761c 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -252,7 +252,7 @@ sub increase_semaphore_count_for_jobid { # used in semaphore propagation
}
-=head2 update_status
+=head2 check_in_job
Arg [1] : $analysis_id
Example :
@@ -263,7 +263,7 @@ sub increase_semaphore_count_for_jobid { # used in semaphore propagation
=cut
-sub update_status {
+sub check_in_job {
my ($self, $job) = @_;
my $sql = "UPDATE job SET status='".$job->status."' ";
@@ -527,7 +527,7 @@ sub gc_dataflow {
$job->dataflow_output_id( $job->input_id() , $branch_name );
- $job->update_status('PASSED_ON');
+ $job->set_and_update_status('PASSED_ON');
if(my $semaphored_job_id = $job->semaphored_job_id) {
$self->decrease_semaphore_count_for_jobid( $semaphored_job_id ); # step-unblock the semaphore
diff --git a/modules/Bio/EnsEMBL/Hive/Process.pm b/modules/Bio/EnsEMBL/Hive/Process.pm
index 99ba89f32..3f1e53430 100644
--- a/modules/Bio/EnsEMBL/Hive/Process.pm
+++ b/modules/Bio/EnsEMBL/Hive/Process.pm
@@ -191,7 +191,7 @@ sub enter_status {
my $job = $self->input_job();
- $job->update_status( $status );
+ $job->set_and_update_status( $status );
my $status_msg = 'Job '.$job->dbID.' : '.$status;
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index 1ebbb6b25..787c036da 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -704,7 +704,7 @@ sub run_one_batch {
} else { # job successfully completed:
$self->more_work_done( $job_partial_timing );
$jobs_done_here++;
- $job->update_status('DONE');
+ $job->set_and_update_status('DONE');
if(my $semaphored_job_id = $job->semaphored_job_id) {
my $dbc = $self->adaptor->db->dbc;
@@ -728,6 +728,17 @@ sub run_one_batch {
}
+sub set_and_update_status {
+ my ($self, $status ) = @_;
+
+ $self->status($status);
+
+ if(my $adaptor = $self->adaptor) {
+ $adaptor->check_in_worker( $self );
+ }
+}
+
+
sub enter_status {
my ($self, $status, $msg) = @_;
@@ -737,8 +748,7 @@ sub enter_status {
$self->worker_say( $msg );
}
- $self->status( $status );
- $self->adaptor->check_in_worker( $self );
+ $self->set_and_update_status( $status );
}
--
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