bugfix: substituting --password for --pass to pacify mysql 5.5.34+ that no...

bugfix: substituting --password for --pass to pacify mysql 5.5.34+ that no longer recognizes options by their prefix

modules/Bio/EnsEMBL/Hive/Params.pm

@@ -310,10 +310,10 @@ sub mysql_conn { # an example stringification formatter (others can be defined h
     my ($self, $db_conn) = @_;
 
     if(ref($db_conn) eq 'HASH') {
-        return "--host=$db_conn->{-host} --port=$db_conn->{-port} --user='$db_conn->{-user}' --pass='$db_conn->{-pass}' $db_conn->{-dbname}";
+        return "--host=$db_conn->{-host} --port=$db_conn->{-port} --user='$db_conn->{-user}' --password='$db_conn->{-pass}' $db_conn->{-dbname}";
     } else {
         my $dbc = go_figure_dbc( $db_conn );
-        return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --pass='".$dbc->password."' ".$dbc->dbname;
+        return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --password='".$dbc->password."' ".$dbc->dbname;
     }
 }
 

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -264,7 +264,7 @@ sub dbconn_2_mysql {    # will save you a lot of typing
     return '--host='.$self->o($db_conn,'-host').' '
           .($port ? '--port='.$self->o($db_conn,'-port').' ' : '')
           .'--user="'.$self->o($db_conn,'-user').'" '
-          .'--pass="'.$self->o($db_conn,'-pass').'" '
+          .'--password="'.$self->o($db_conn,'-pass').'" '
           .($with_db ? ($self->o($db_conn,'-dbname').' ') : '');
 }
 

modules/Bio/EnsEMBL/Hive/RunnableDB/DatabaseDumper.pm

@@ -205,7 +205,7 @@ sub run {
 sub mysql_conn_from_dbc {
     my ($self, $dbc) = @_; 
 
-    return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --pass='".$dbc->password."' ".$dbc->dbname;
+    return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --password='".$dbc->password."' ".$dbc->dbname;
 }
 
 

modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm

@@ -196,7 +196,7 @@ sub get_row_count {
 sub mysql_conn_from_dbc {
     my ($self, $dbc) = @_;
 
-    return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --pass='".$dbc->password."' ".$dbc->dbname;
+    return '--host='.$dbc->host.' --port='.$dbc->port." --user='".$dbc->username."' --password='".$dbc->password."' ".$dbc->dbname;
 }
 
 1;

scripts/db_cmd.pl

@@ -128,7 +128,7 @@ sub dbc_hash_to_cmd {
         $cmd = ($to_params ? '' : 'mysql ')
               ."--host=$dbc_hash->{host} "
               .(defined($dbc_hash->{port}) ? "--port=$dbc_hash->{port} " : '')
-              ."--user=$dbc_hash->{user} --pass='$dbc_hash->{pass}' "
+              ."--user=$dbc_hash->{user} --password='$dbc_hash->{pass}' "
               .(defined($extra) ? "$extra " : '')
               .($dbc_hash->{dbname} || '')
               .(defined($sqlcmd) ? " -e '$sqlcmd'" : '');