stringification and evaluation of pipeline-wide(meta) parameters

modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm

@@ -109,6 +109,13 @@ sub _parse_meta {
     my $sth = $self->db->dbc()->prepare("SELECT meta_key, meta_value FROM meta ORDER BY meta_id");
     $sth->execute();
     while (my ($meta_key, $meta_value)=$sth->fetchrow_array()) {
+        if($meta_value=~/^'.*'$/
+        or $meta_value=~/^".*"$/
+        or $meta_value=~/^{.*}$/
+        or $meta_value=~/^[.*]$/) {
+
+            $meta_value = eval($meta_value);
+        }
         $meta_params_hash{$meta_key} = $meta_value;
     }
     $sth->finish();

scripts/init_pipeline.pl

@@ -17,6 +17,14 @@ sub dbconn_2_url {
     return "mysql://$db_conn->{-user}:$db_conn->{-pass}\@$db_conn->{-host}:$db_conn->{-port}/$db_conn->{-dbname}";
 }
 
+sub dbconn_2_mysql {    # used by pipeline configuration files themselves
+    my ($db_conn, $with_db) = @_;
+
+    return "--host=$db_conn->{-host} --port=$db_conn->{-port} "
+          ."--user=$db_conn->{-user} --pass=$db_conn->{-pass} "
+          .($with_db ? "--database=$db_conn->{-dbname} " : '');
+}
+
 sub main {
 
     my $topup_flag  = 0;  # do not run initial scripts and only add new analyses+jobs (ignore the fetchable analyses)
@@ -57,7 +65,7 @@ sub main {
             if($topup_flag) {
                 $meta_container->delete_key($meta_key);
             }
-            $meta_container->store_key_value($meta_key, $meta_value);
+            $meta_container->store_key_value($meta_key, stringify($meta_value));
         }
 
         warn "Done.\n\n";