From 19168ee48c634baf7cf6e23e6b19686e76e54af8 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 1 Jul 2014 15:53:23 +0100
Subject: [PATCH] improved and simplified logging/reporting
---
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 22 ------------
modules/Bio/EnsEMBL/Hive/Process.pm | 47 +++++++++++++++++++------
modules/Bio/EnsEMBL/Hive/Worker.pm | 6 ++--
3 files changed, 38 insertions(+), 37 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 89d49059f..4db6a33a5 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -238,28 +238,6 @@ sub died_somewhere {
##-----------------[/indicators to the Worker]-------------------------------
-=head2 warning
-
- Description: records a non-error message in 'log_message' table linked to the current job
-
-=cut
-
-sub warning {
- my ($self, $msg, $is_error) = @_;
-
- $is_error //= 0;
- my $job_adaptor = $self->adaptor;
-
- if( $is_error or !$job_adaptor) {
- my $class = $is_error ? 'Error' : 'Warning';
- print STDERR "Job${class}: $msg\n";
- }
-
- if( $job_adaptor ) {
- $job_adaptor->db->get_LogMessageAdaptor()->store_job_message($self->dbID, $msg, $is_error);
- }
-}
-
sub fan_cache { # a self-initializing getter (no setting)
# Returns a hash-of-lists { 2 => [list of jobs waiting to be funneled into 2], 3 => [list of jobs waiting to be funneled into 3], etc}
diff --git a/modules/Bio/EnsEMBL/Hive/Process.pm b/modules/Bio/EnsEMBL/Hive/Process.pm
index 7386d9e1f..935dff3a8 100644
--- a/modules/Bio/EnsEMBL/Hive/Process.pm
+++ b/modules/Bio/EnsEMBL/Hive/Process.pm
@@ -145,7 +145,7 @@ sub life_cycle {
$self->write_output;
$job_partial_timing{'WRITE_OUTPUT'} = $partial_stopwatch->get_elapsed();
} else {
- print STDERR "\n!!! *no* WRITE_OUTPUT requested, so there will be no AUTOFLOW\n" if($self->debug);
+ $self->say_with_header( ": *no* WRITE_OUTPUT requested, so there will be no AUTOFLOW" );
}
};
@@ -169,7 +169,7 @@ sub life_cycle {
unless( $job->died_somewhere ) {
if( $self->execute_writes and $job->autoflow ) { # AUTOFLOW doesn't have its own status so will have whatever previous state of the job
- print STDERR "\njob ".$job->dbID." : AUTOFLOW input->output\n" if($self->debug);
+ $self->say_with_header( ': AUTOFLOW input->output' );
$job->dataflow_output_id();
}
@@ -186,6 +186,21 @@ sub life_cycle {
}
+sub say_with_header {
+ my ($self, $msg, $important) = @_;
+
+ $important //= $self->debug();
+
+ if($important) {
+ if(my $worker = $self->worker) {
+ $worker->worker_say( $msg );
+ } else {
+ print STDERR "StandaloneJob $msg\n";
+ }
+ }
+}
+
+
sub enter_status {
my ($self, $status) = @_;
@@ -194,9 +209,25 @@ sub enter_status {
$job->set_and_update_status( $status );
if(my $worker = $self->worker) {
- $worker->enter_status( $status );
- } elsif($self->debug) {
- print STDERR "StandaloneJob : $status\n";
+ $worker->set_and_update_status( $status );
+ }
+
+ $self->say_with_header( '-> '.$status );
+}
+
+
+sub warning {
+ my ($self, $msg, $is_error) = @_;
+
+ $is_error //= 0;
+ chomp $msg;
+
+ $self->say_with_header( ($is_error ? 'Fatal' : 'Warning')." : $msg" );
+
+ my $job = $self->input_job;
+
+ if(my $job_adaptor = $job->adaptor) {
+ $job_adaptor->db->get_LogMessageAdaptor()->store_job_message($job->dbID, $msg, $is_error);
}
}
@@ -471,12 +502,6 @@ sub param_substitute {
return $self->input_job->param_substitute(@_);
}
-sub warning {
- my $self = shift @_;
-
- return $self->input_job->warning(@_);
-}
-
sub dataflow_output_id {
my $self = shift @_;
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index e33048ecb..1392fecca 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -743,12 +743,10 @@ sub set_and_update_status {
sub enter_status {
- my ($self, $status, $msg) = @_;
-
- $msg ||= ": $status";
+ my ($self, $status) = @_;
if($self->debug) {
- $self->worker_say( $msg );
+ $self->worker_say( '-> '.$status );
}
$self->set_and_update_status( $status );
--
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