interface_change: protected_prepare_execute() takes all sql-related parameters as first argument

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -248,7 +248,7 @@ sub decrease_semaphore_count_for_jobid {    # used in semaphore annihilation or
         WHERE job_id=? AND status='SEMAPHORED'
     };
     
-    $self->dbc->protected_prepare_execute( $sql, $dec, $jobid );
+    $self->dbc->protected_prepare_execute( [ $sql, $dec, $jobid ] );
 }
 
 sub increase_semaphore_count_for_jobid {    # used in semaphore propagation
@@ -262,7 +262,7 @@ sub increase_semaphore_count_for_jobid {    # used in semaphore propagation
         WHERE job_id=?
     };
     
-    $self->dbc->protected_prepare_execute( $sql, $inc, $jobid );
+    $self->dbc->protected_prepare_execute( [ $sql, $inc, $jobid ] );
 }
 
 
@@ -294,7 +294,7 @@ sub check_in_job {
     $sql .= " WHERE job_id='".$job->dbID."' ";
 
         # This particular query is infamous for collisions and 'deadlock' situations; let's wait and retry:
-    $self->dbc->protected_prepare_execute( $sql );
+    $self->dbc->protected_prepare_execute( [ $sql ] );
 }
 
 
@@ -416,9 +416,9 @@ sub grab_jobs_for_role {
     };
 
         # we have to be explicitly numeric here because of '0E0' value returned by DBI if "no rows have been affected":
-    if(  (my $claim_count = $self->dbc->protected_prepare_execute( $prefix_sql . $virgin_sql . $limit_sql . $offset_sql . $suffix_sql)) == 0 ) {
-        if( ($claim_count = $self->dbc->protected_prepare_execute( $prefix_sql .               $limit_sql . $offset_sql . $suffix_sql)) == 0 ) {
-             $claim_count = $self->dbc->protected_prepare_execute( $prefix_sql .               $limit_sql .               $suffix_sql);
+    if(  (my $claim_count = $self->dbc->protected_prepare_execute( [ $prefix_sql . $virgin_sql . $limit_sql . $offset_sql . $suffix_sql ] )) == 0 ) {
+        if( ($claim_count = $self->dbc->protected_prepare_execute( [ $prefix_sql .               $limit_sql . $offset_sql . $suffix_sql ] )) == 0 ) {
+             $claim_count = $self->dbc->protected_prepare_execute( [ $prefix_sql .               $limit_sql .               $suffix_sql ] );
         }
     }
 

modules/Bio/EnsEMBL/Hive/DBSQL/DBConnection.pm

@@ -115,7 +115,9 @@ sub url {
 
 sub protected_prepare_execute {     # try to resolve certain mysql "Deadlocks" by trying again (a useful workaround even in mysql 5.1.61)
     my $self        = shift @_;
-    my $sql         = shift @_;
+    my $sql_params  = shift @_;
+
+    my $sql_cmd     = shift @$sql_params;
 
     my $attempts        = 4;
     my $sleep_max_sec   = 1;
@@ -125,8 +127,8 @@ sub protected_prepare_execute {     # try to resolve certain mysql "Deadlocks" b
 
     foreach my $attempt (1..$attempts) {
         eval {
-            my $sth = $self->prepare($sql);
-            $retval = $sth->execute( @_ );
+            my $sth = $self->prepare( $sql_cmd );
+            $retval = $sth->execute( @$sql_params );
             $sth->finish;
             1;
         } or do {
@@ -142,7 +144,7 @@ sub protected_prepare_execute {     # try to resolve certain mysql "Deadlocks" b
                 }
 
                 my $this_sleep_sec = rand( $sleep_max_sec );
-                $log_message_adaptor->store_hive_message( "Caught a DEADLOCK when trying to execute '$sql' (attempt #$attempt), retrying in $this_sleep_sec sec", 0 );
+                $log_message_adaptor->store_hive_message( "Caught a DEADLOCK when trying to execute '$sql_cmd' (attempt #$attempt), retrying in $this_sleep_sec sec", 0 );
 
                 usleep( $this_sleep_sec*1000000 );
                 $sleep_max_sec *= 2;
@@ -152,7 +154,7 @@ sub protected_prepare_execute {     # try to resolve certain mysql "Deadlocks" b
         };
         last;
     }
-    die "After $attempts attempts the query '$sql' is still in a deadlock: $@" if($@);
+    die "After $attempts attempts the query '$sql_cmd' is still in a deadlock: $@" if($@);
 
     return $retval;
 }