[Bioperl-l] Bio::DB::GFF::Adaptor::dbi.pm schema creation

[Brian Desany]

Lincoln,

I'm exploring the GFF modules you wrote, and while running load_gff.pl I
noticed that it was hanging on Oracle (8.1.7.0.1 on Linux) in the middle of
the script.

It seems that (at least this version of) Oracle doesn't like it when you try
to create a trigger that references a sequence that doesn't exist, as
Bio::DB::GFF::Adaptor::dbi::create_other_schema_objects tries to do.

The method creates the schema objects in no particular order, but if you
create them in sorted order then conveniently, 'sequence' comes before
'trigger' and everything is created properly.

To give you specific orientation:

*** BioPerlRoot/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm  Thu Oct 24 08:59:56
2002
--- BioPerlRoot/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm-orig     Thu Oct 24
09:27:46 2002
***************
*** 924,930 ****
    #my $schema = $self->schema;

    #foreach my $object_type(keys $$schema{$table_name}){
!    foreach my $object_type(sort keys %$table_schema){
      if ($object_type !~ 'table') {
       foreach my $object_name(keys %{$table_schema->{$object_type}}){
          my $create_object_stmt =
$table_schema->{$object_type}{$object_name};
--- 924,930 ----
    #my $schema = $self->schema;

    #foreach my $object_type(keys $$schema{$table_name}){
!    foreach my $object_type(keys %$table_schema){
      if ($object_type !~ 'table') {
       foreach my $object_name(keys %{$table_schema->{$object_type}}){
          my $create_object_stmt =
$table_schema->{$object_type}{$object_name};


I didn't commit this because I don't know if it would screw up the mysql
part of it, plus it's a 'fix by coincidence'.

Should I make this change anyway?

-Brian.
--------------------------------------------
Brian A. Desany, Ph.D.
Dictyostelium Genome Sequencing Project
Baylor College of Medicine
bdesany@bcm.tmc.edu
(713)798-5639
http://www.dictygenome.org
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