From ade5f4271d2fce0a4f8d67f67b162857179f7a50 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Thu, 22 Nov 2012 17:21:22 +0000
Subject: [PATCH] Introduced a new 'NO_ROLE' cause_of_death for failures during
specialization (not so much of an error, really!)
---
modules/Bio/EnsEMBL/Hive/Queen.pm | 11 ++++++-----
modules/Bio/EnsEMBL/Hive/Worker.pm | 4 ++--
sql/patch_2012-11-22.sql | 3 +++
sql/tables.sql | 2 +-
sql/tables.sqlite | 2 +-
5 files changed, 13 insertions(+), 9 deletions(-)
create mode 100644 sql/patch_2012-11-22.sql
diff --git a/modules/Bio/EnsEMBL/Hive/Queen.pm b/modules/Bio/EnsEMBL/Hive/Queen.pm
index 1328c3306..32bc9de7e 100644
--- a/modules/Bio/EnsEMBL/Hive/Queen.pm
+++ b/modules/Bio/EnsEMBL/Hive/Queen.pm
@@ -254,15 +254,15 @@ sub specialize_new_worker {
die "Analysis is DONE, and doesn't require workers";
}
}
-
- } else { # probably scheduled by beekeeper.pl
-
- $stats = $self->suggest_analysis_to_specialize_by_rc_id_meadow_type($worker->resource_class_id, $worker->meadow_type)
- or die "Queen failed to pick an analysis for the worker";
+ # probably scheduled by beekeeper.pl:
+ } elsif( $stats = $self->suggest_analysis_to_specialize_by_rc_id_meadow_type($worker->resource_class_id, $worker->meadow_type) ) {
print "Queen picked analysis with dbID=".$stats->analysis_id." for the worker\n";
$analysis_id = $stats->analysis_id;
+ } else {
+ $worker->cause_of_death('NO_ROLE');
+ die "No analysis suitable for the worker was found\n";
}
# now set it in the $worker:
@@ -323,6 +323,7 @@ sub register_worker_death {
or $cod eq 'RUNLIMIT'
or $cod eq 'KILLED_BY_USER'
or $cod eq 'SEE_MSG'
+ or $cod eq 'NO_ROLE'
or $cod eq 'CONTAMINATED') {
$self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
}
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index 08634df11..a88229ce2 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -523,8 +523,8 @@ sub run {
$min_batch_time = $self->analysis->stats->min_batch_time();
1;
} or do {
- my $msg = "Could not specialize worker:\n\t".$@;
- warn "$msg\n";
+ my $msg = $@;
+ warn "Could not specialize worker:\n\t$msg\n";
$self->adaptor->db->get_JobMessageAdaptor()->store_worker_message($self->dbID, $msg, 1 );
$self->cause_of_death('SEE_MSG') unless($self->cause_of_death()); # some specific causes could have been set prior to die "...";
diff --git a/sql/patch_2012-11-22.sql b/sql/patch_2012-11-22.sql
new file mode 100644
index 000000000..7e8dc87f2
--- /dev/null
+++ b/sql/patch_2012-11-22.sql
@@ -0,0 +1,3 @@
+ # add 'NO_ROLE' cause_of_death specifically for workers that could not specialize
+ALTER TABLE worker MODIFY COLUMN cause_of_death enum('NO_ROLE', 'NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'SEE_MSG', 'UNKNOWN') DEFAULT NULL;
+
diff --git a/sql/tables.sql b/sql/tables.sql
index 5c8a04d18..7503f2e18 100644
--- a/sql/tables.sql
+++ b/sql/tables.sql
@@ -85,7 +85,7 @@ CREATE TABLE worker (
born timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
last_check_in datetime NOT NULL,
died datetime DEFAULT NULL,
- cause_of_death enum('NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'SEE_MSG', 'UNKNOWN') DEFAULT NULL,
+ cause_of_death enum('NO_ROLE', 'NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'SEE_MSG', 'UNKNOWN') DEFAULT NULL,
log_dir varchar(255) DEFAULT NULL,
PRIMARY KEY (worker_id),
diff --git a/sql/tables.sqlite b/sql/tables.sqlite
index eda95f048..813a391ac 100644
--- a/sql/tables.sqlite
+++ b/sql/tables.sqlite
@@ -77,7 +77,7 @@ CREATE TABLE worker (
born timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
last_check_in datetime NOT NULL,
died datetime DEFAULT NULL,
- cause_of_death TEXT DEFAULT NULL, /* enum('NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'SEE_MSG', 'UNKNOWN') DEFAULT NULL */
+ cause_of_death TEXT DEFAULT NULL, /* enum('NO_ROLE', 'NO_WORK', 'JOB_LIMIT', 'HIVE_OVERLOAD', 'LIFESPAN', 'CONTAMINATED', 'KILLED_BY_USER', 'MEMLIMIT', 'RUNLIMIT', 'SEE_MSG', 'UNKNOWN') DEFAULT NULL */
log_dir varchar(80) DEFAULT NULL
);
--
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