From a27cac4bd002f178c5db01cfa2af207a4e55fa5d Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Mon, 14 Jun 2010 23:06:46 +0000
Subject: [PATCH] track insert_ids of separate commands and make them available
for dataflow
---
modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm | 32 ++++++++++++-------
1 file changed, 21 insertions(+), 11 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
index 8fcc1000c..b19ef1439 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
@@ -91,16 +91,9 @@ sub fetch_input {
? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID( $self->param('did') )
: die "Could not find the command defined in input_id(), param('sql') or param('did')";
- # Perform parameter substitution:
+ # Store the sql command array:
#
- my @substituted_sqls = ();
- foreach my $unsubst ((ref($sql) eq 'ARRAY') ? @$sql : ($sql) ) {
- push @substituted_sqls, $self->param_substitute($unsubst);
- }
-
- # Store the substituted sql command array
- #
- $self->param('sqls', \@substituted_sqls);
+ $self->param('sqls', (ref($sql) eq 'ARRAY') ? $sql : [$sql] );
# Use connection parameters to another database if supplied, otherwise use the current database as default:
#
@@ -126,20 +119,37 @@ sub run {
my $dbc = $self->param('dbc');
my $sqls = $self->param('sqls');
+ my %output_id;
+
# What would be a generic way of indicating an error in (My)SQL statement, that percolates through PerlDBI?
- foreach my $sql (@$sqls) {
+ my $counter = 0;
+ foreach my $unsubst_sql (@$sqls) {
+
+ # Perform parameter substitution:
+ my $sql = $self->param_substitute($unsubst_sql);
+
$dbc->do( $sql );
+
+ my $insert_id_name = '_insert_id_'.$counter++;
+ my $insert_id_value = $dbc->db_handle->{'mysql_insertid'};
+ $output_id{$insert_id_name} = $insert_id_value;
+ $self->param($insert_id_name, $insert_id_value); # for templates
}
+
+ $self->param('output_id', \%output_id);
}
=head2 write_output
Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
- Here we have nothing to do, as the wrapper is very generic.
+ Here we only flow out the insert_ids.
=cut
sub write_output {
+ my $self = shift;
+
+ $self->dataflow_output_id( $self->param('output_id'), 2);
}
1;
--
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