Merge branch 'version/2.1' into version/2.2

modules/Bio/EnsEMBL/Hive/Meadow.pm

@@ -167,6 +167,19 @@ sub parse_report_source_line {
     return;
 }
 
+=head2 get_report_entries_for_process_ids
+    Title   :  get_report_entries_for_process_ids
+    Function:  A higher-level method that gets process_ids as input and
+               returns a structure like parse_report_source_line.
+=cut
+
+sub get_report_entries_for_process_ids {
+    my ($self, @process_ids) = @_;
+
+    warn "\t".ref($self)." does not support resource usage logs\n";
+
+    return;
+}
 
 sub get_report_entries_for_time_interval {
     my $self = shift @_;

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

@@ -280,14 +280,16 @@ sub get_report_entries_for_process_ids {
 
     my %combined_report_entries = ();
 
-    while (my $pid_batch = join(' ', map { "'$_'" } splice(@_, 0, 20))) {  # can't fit too many pids on one shell cmdline
-        my $cmd = "bacct -l $pid_batch |";
+    unless ($self->config_get('AccountingDisabled')) {
+        while (my $pid_batch = join(' ', map { "'$_'" } splice(@_, 0, 20))) {  # can't fit too many pids on one shell cmdline
+            my $cmd = "bacct -l $pid_batch |";
 
-#        warn "LSF::get_report_entries_for_process_ids() running cmd:\n\t$cmd\n";
+#           warn "LSF::get_report_entries_for_process_ids() running cmd:\n\t$cmd\n";
 
-        my $batch_of_report_entries = $self->parse_report_source_line( $cmd );
+            my $batch_of_report_entries = $self->parse_report_source_line( $cmd );
 
-        %combined_report_entries = (%combined_report_entries, %$batch_of_report_entries);
+            %combined_report_entries = (%combined_report_entries, %$batch_of_report_entries);
+        }
     }
 
     return \%combined_report_entries;
@@ -297,17 +299,21 @@ sub get_report_entries_for_process_ids {
 sub get_report_entries_for_time_interval {
     my ($self, $from_time, $to_time, $username) = @_;
 
-    my $from_timepiece = Time::Piece->strptime($from_time, '%Y-%m-%d %H:%M:%S');
-    $from_time = $from_timepiece->strftime('%Y/%m/%d/%H:%M');
+    my $batch_of_report_entries = {};
+
+    unless ($self->config_get('AccountingDisabled')) {
+        my $from_timepiece = Time::Piece->strptime($from_time, '%Y-%m-%d %H:%M:%S');
+        $from_time = $from_timepiece->strftime('%Y/%m/%d/%H:%M');
 
-    my $to_timepiece = Time::Piece->strptime($to_time, '%Y-%m-%d %H:%M:%S') + 2*ONE_MINUTE;
-    $to_time = $to_timepiece->strftime('%Y/%m/%d/%H:%M');
+        my $to_timepiece = Time::Piece->strptime($to_time, '%Y-%m-%d %H:%M:%S') + 2*ONE_MINUTE;
+        $to_time = $to_timepiece->strftime('%Y/%m/%d/%H:%M');
 
-    my $cmd = "bacct -l -C $from_time,$to_time ".($username ? "-u $username" : '') . ' |';
+        my $cmd = "bacct -l -C $from_time,$to_time ".($username ? "-u $username" : '') . ' |';
 
 #        warn "LSF::get_report_entries_for_time_interval() running cmd:\n\t$cmd\n";
 
-    my $batch_of_report_entries = $self->parse_report_source_line( $cmd );
+        $batch_of_report_entries = $self->parse_report_source_line( $cmd );
+    }
 
     return $batch_of_report_entries;
 }

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -362,17 +362,16 @@ sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but i
         if(my $lost_this_meadow = scalar(keys %$pid_to_lost_worker) ) {
             warn "GarbageCollector:\tDiscovered $lost_this_meadow lost $meadow_type Workers\n";
 
-            my $report_entries = {};
+            my $report_entries;
 
             if($this_meadow->can('find_out_causes')) {
                 die "Your Meadow::$meadow_type driver now has to support get_report_entries_for_process_ids() method instead of find_out_causes(). Please update it.\n";
 
-            } elsif($this_meadow->can('get_report_entries_for_process_ids')) {
-                $report_entries = $this_meadow->get_report_entries_for_process_ids( keys %$pid_to_lost_worker );
-                my $lost_with_known_cod = scalar( grep { $_->{'cause_of_death'} } values %$report_entries);
-                warn "GarbageCollector:\tFound why $lost_with_known_cod of $meadow_type Workers died\n";
             } else {
-                warn "GarbageCollector:\t$meadow_type meadow does not support post-mortem examination\n";
+                if ($report_entries = $this_meadow->get_report_entries_for_process_ids( keys %$pid_to_lost_worker )) {
+                    my $lost_with_known_cod = scalar( grep { $_->{'cause_of_death'} } values %$report_entries);
+                    warn "GarbageCollector:\tFound why $lost_with_known_cod of $meadow_type Workers died\n";
+                }
             }
 
             warn "GarbageCollector:\tReleasing the jobs\n";

t/04.meadow/lsf.t

@@ -21,7 +21,7 @@ use warnings;
 use Cwd;
 use File::Basename;
 
-use Test::More tests => 18;
+use Test::More;
 use Test::Exception;
 
 use Bio::EnsEMBL::Hive::Utils::Config;
@@ -183,17 +183,32 @@ my $expected_bacct = {
     },
 };
 
+unless ($lsf_meadow->config_get('AccountingDisabled')) {
+    lives_and( sub {
+        local $ENV{EHIVE_EXPECTED_BACCT} = '-l 34 56[7]';
+        my $h = $lsf_meadow->get_report_entries_for_process_ids(34, '56[7]');
+        is_deeply($h, $expected_bacct, 'Got bacct output');
+    }, 'Can call bacct on process_ids');
+
+    lives_and( sub {
+        local $ENV{EHIVE_EXPECTED_BACCT} = '-l -C 2015/10/11/12:23,2015/12/12/23:58 -u kb3';
+        my $h = $lsf_meadow->get_report_entries_for_time_interval('2015-10-11 12:23:45', '2015-12-12 23:56:59', 'kb3');
+        is_deeply($h, $expected_bacct, 'Got bacct output');
+    }, 'Can call bacct on a date range');
+}
+
+$lsf_meadow->config_set("AccountingDisabled", 1);
 lives_and( sub {
     local $ENV{EHIVE_EXPECTED_BACCT} = '-l 34 56[7]';
     my $h = $lsf_meadow->get_report_entries_for_process_ids(34, '56[7]');
-    is_deeply($h, $expected_bacct, 'Got bacct output');
-}, 'Can call bacct on process_ids');
+    is_deeply($h, {}, 'No bacct output when accounting disabled');
+}, 'Suppressed bacct when AccountingDisabled when checking process_ids');
 
 lives_and( sub {
     local $ENV{EHIVE_EXPECTED_BACCT} = '-l -C 2015/10/11/12:23,2015/12/12/23:58 -u kb3';
     my $h = $lsf_meadow->get_report_entries_for_time_interval('2015-10-11 12:23:45', '2015-12-12 23:56:59', 'kb3');
-    is_deeply($h, $expected_bacct, 'Got bacct output');
-}, 'Can call bacct on a date range');
+    is_deeply($h, {}, 'No bacct output when accounting disabled');
+}, 'Suppressed bacct when AccountingDisabled when checking a date range');
 
 done_testing();