Support extra parameters added to the client's command line

scripts/db_conn.pl

@@ -18,7 +18,7 @@ use Bio::EnsEMBL::Hive::Utils ('script_usage');
 
 
 sub main {
-    my ($reg_conf, $reg_type, $reg_alias, $url, $sqlcmd, $verbose, $help);
+    my ($reg_conf, $reg_type, $reg_alias, $url, $sqlcmd, $extra, $verbose, $help);
 
     GetOptions(
                 # connect to the database:
@@ -29,6 +29,7 @@ sub main {
             'url=s'             => \$url,
 
             'sqlcmd=s'          => \$sqlcmd,
+            'extra=s'           => \$extra,
 
             'verbose!'          => \$verbose,
             'help!'             => \$help,
@@ -61,7 +62,7 @@ sub main {
         script_usage(1);
     }
 
-    my $cmd = dbc_hash_to_cmd( $dbc_hash, $sqlcmd );
+    my $cmd = dbc_hash_to_cmd( $dbc_hash, $sqlcmd, $extra );
 
     print "\nRunning command:\t$cmd\n\n" if($verbose);
 
@@ -69,7 +70,9 @@ sub main {
 }
 
 sub dbc_hash_to_cmd {
-    my ($dbc_hash, $sqlcmd) = @_;
+    my ($dbc_hash, $sqlcmd, $extra) = @_;
+
+    $extra ||= '';
 
     my $cmd;
 
@@ -79,7 +82,7 @@ sub dbc_hash_to_cmd {
 
         $cmd = "mysql --host=$dbc_hash->{host} "
               .(defined($dbc_hash->{port}) ? "--port=$dbc_hash->{port}" : '')
-              ." --user='$dbc_hash->{user}' --pass='$dbc_hash->{pass}' $dbc_hash->{dbname}"
+              ." --user='$dbc_hash->{user}' --pass='$dbc_hash->{pass}' $extra $dbc_hash->{dbname}"
               .(defined($sqlcmd) ? " -e '$sqlcmd'" : '');
     } elsif($driver eq 'pgsql') {
 
@@ -87,11 +90,11 @@ sub dbc_hash_to_cmd {
               .(defined($dbc_hash->{port}) ? "--port=$dbc_hash->{port}" : '')
               ." --username='$dbc_hash->{user}'"
               .(defined($sqlcmd) ? " --command='$sqlcmd'" : '')
-              ." $dbc_hash->{dbname}";
+              ." $extra $dbc_hash->{dbname}";
     } elsif($driver eq 'sqlite') {
 
         if($dbc_hash->{dbname}) {
-            $cmd = "sqlite3 $dbc_hash->{dbname}"
+            $cmd = "sqlite3 $extra $dbc_hash->{dbname}"
                   .(defined($sqlcmd) ? " '$sqlcmd'" : '');
         } elsif($sqlcmd =~ /DROP\s+DATABASE\s+(?:IF\s+EXISTS\s+)?(\w+)/i ) {
             $cmd = "rm -f $1";
@@ -116,7 +119,7 @@ __DATA__
 
 =head1 SYNOPSIS
 
-    db_conn.pl {-url <url> | -reg_conf <reg_conf> -reg_alias <reg_alias> [-reg_type <reg_type>] } [ -sql <sql_command> ] [ -verbose ]
+    db_conn.pl {-url <url> | -reg_conf <reg_conf> -reg_alias <reg_alias> [-reg_type <reg_type>] } [ -sql <sql_command> ] [ -extra <extra_params> ] [ -verbose ]
 
 =head1 DESCRIPTION
 
@@ -126,7 +129,7 @@ __DATA__
 
     db_conn.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/" -sql 'CREATE DATABASE lg4_long_mult'
     db_conn.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult"
-    db_conn.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult" -sql 'SELECT * FROM analysis_base'
+    db_conn.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult" -sql 'SELECT * FROM analysis_base' -extra='--html'
 
     db_conn.pl -reg_conf ${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/scripts/pipeline/production_reg_conf.pl -reg_alias compara_master -reg_type compara
     db_conn.pl -reg_conf ${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/scripts/pipeline/production_reg_conf.pl -reg_alias compara_prev   -reg_type compara