switched to using Time::Piece instead of potentially driver-dependent datetime functions

Conflicts:
	scripts/generate_timeline.pl

scripts/generate_timeline.pl

@@ -18,6 +18,8 @@ use Getopt::Long;
 use List::Util qw(sum);
 use POSIX;
 use Data::Dumper;
+use Time::Piece;
+use Time::Seconds;  # not sure if seconds-only arithmetic also needs it
 
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('script_usage');
@@ -148,12 +150,21 @@ sub main {
     # Get the events from the database
     my %events = ();
     if ($mode ne 'pending_workers') {
-        my @tmp_dates = @{$dbh->selectall_arrayref('SELECT DATE_FORMAT(when_started, "%Y-%m-%dT%T"), DATE_FORMAT(when_finished, "%Y-%m-%dT%T"), analysis_id, worker_id, resource_class_id FROM role JOIN worker USING (worker_id)')};
+        my @tmp_dates = @{$dbh->selectall_arrayref('SELECT when_started, when_finished, analysis_id, worker_id FROM role JOIN worker USING (worker_id)')};
         warn scalar(@tmp_dates), " events\n" if $verbose;
 
         foreach my $db_entry (@tmp_dates) {
-            my ($birth_date, $death_date, $analysis_id, $worker_id, $resource_class_id) = @$db_entry;
+            my ($when_started, $when_finished, $analysis_id, $worker_id, $resource_class_id) = @$db_entry;
             $resource_class_id //= $default_resource_class{$analysis_id};
+
+                # temporary Time::Piece values
+            my $birth_datetime = Time::Piece->strptime( $when_started,  '%Y-%m-%d %H:%M:%S');
+            my $death_datetime = Time::Piece->strptime( $when_finished, '%Y-%m-%d %H:%M:%S');
+
+                # string values:
+            my $birth_date = $birth_datetime->date . 'T' . $birth_datetime->hms;
+            my $death_date = $death_datetime->date . 'T' . $death_datetime->hms;
+
             my $offset = 0;
 
             if ($mode eq 'workers') {
@@ -175,11 +186,20 @@ sub main {
             $events{$death_date}{$analysis_id} -= $offset if ($offset > 0) and $death_date;
         }
     } else {
-        my @tmp_dates = @{$dbh->selectall_arrayref('SELECT DATE_FORMAT(DATE_SUB(min(when_started), INTERVAL pending_sec SECOND), "%Y-%m-%dT%T"), DATE_FORMAT(min(when_started), "%Y-%m-%dT%T"), analysis_id FROM role JOIN worker_resource_usage USING (worker_id) WHERE pending_sec IS NOT NULL AND pending_sec > 0 GROUP BY worker_id')};
+        my @tmp_dates = @{$dbh->selectall_arrayref('SELECT min(when_started), pending_sec, analysis_id FROM role JOIN worker_resource_usage USING (worker_id) WHERE pending_sec IS NOT NULL AND pending_sec > 0 GROUP BY worker_id')};
         warn scalar(@tmp_dates), " events\n" if $verbose;
 
         foreach my $db_entry (@tmp_dates) {
-            my ($start_pending, $start_running, $analysis_id) = @$db_entry;
+            my ($when_started, $pending_sec, $analysis_id) = @$db_entry;
+
+                # temporary Time::Piece values
+            my $submitted_datetime = Time::Piece->strptime( $when_started, '%Y-%m-%d %H:%M:%S') - $pending_sec;
+            my $started_datetime   = Time::Piece->strptime( $when_started, '%Y-%m-%d %H:%M:%S');
+
+                # string values:
+            my $start_pending = $submitted_datetime->date . 'T' . $submitted_datetime->hms;
+            my $start_running = $started_datetime->date   . 'T' . $started_datetime->hms;
+
             $events{$start_pending}{$analysis_id} += 1;
             $events{$start_running}{$analysis_id} -= 1;
         }