# -*-Perl-*-
# $Id: 16obda.t,v 1.4 2006/09/25 16:07:43 bosborne Exp $
use lib 't';
use vars qw($old_obda_path);
BEGIN {
    # to handle systems with no installed Test module
    # we include the t dir (where a copy of Test.pm is located)
    # as a fallback
    eval { require Test; };
    use Test;    
    plan tests => 12;
         $old_obda_path = $ENV{OBDA_SEARCH_PATH} 
                if defined $ENV{OBDA_SEARCH_PATH};
         $ENV{OBDA_SEARCH_PATH} = 't/data/';
}
use strict;
use DBTestHarness;
use Bio::SeqIO;
use Bio::Root::IO;
use Bio::DB::Persistent::BioNamespace;
use Bio::DB::Registry;
my $biosql = DBTestHarness->new("biosql");
my $db = $biosql->get_DBAdaptor();
ok $db;
my $registry_file = "t/data/seqdatabase.ini";
my $obda_name = "mytestbiosql";
# create a temporary seqdatabase.ini file specific for this test database
write_registry($registry_file);
my $seqio = Bio::SeqIO->new('-format' => 'genbank',
                            '-file' => Bio::Root::IO->catfile(
                                                      't','data','parkin.gb'));
my $seq = $seqio->next_seq();
ok $seq;
my $pseq = $db->create_persistent($seq);
$pseq->namespace("mytestnamespace");
$pseq->store(); # this will raise warnings if there are duplicates
ok $pseq->primary_key();
$pseq->commit;
# try/finally block
eval {
        my $registry = Bio::DB::Registry->new;
        ok $registry;
        my $biodb = $registry->get_database($obda_name);
        ok $biodb;
        my $seq = $biodb->get_Seq_by_acc('AB019558');
        ok $seq->primary_id, 5456929;
        $seq = $biodb->get_Seq_by_id(5456929);
        ok $seq->accession, "AB019558";
        $seq = $biodb->get_Seq_by_version('AB019558.1');
        ok $seq->primary_id, 5456929;
};
print STDERR $@ if $@;
# delete seq
ok ($pseq->remove(), 1);
my $ns = Bio::DB::Persistent::BioNamespace->new(-identifiable => $pseq);
ok $ns = $db->get_object_adaptor($ns)->find_by_unique_key($ns);
ok $ns->primary_key();
ok ($ns->remove(), 1);
$ns->commit;
END {
        unlink $registry_file if (-e $registry_file);
        $ENV{OBDA_SEARCH_PATH} = $old_obda_path if defined $old_obda_path;
}
sub write_registry {
        my $file = shift;
        my $c = $db->dbcontext;
        my ($host,$port,$dbname,$pass,$user,$driver) =
         ($c->host,$c->port,$c->dbname,$c->password,$c->username,$c->driver);
        my $text = "VERSION=1.00
[$obda_name]
protocol=biosql
location=$host:$port
dbname=$dbname
passwd=$pass
user=$user
driver=$driver
";
   open F,">$file";
        print F $text;
   close F;
}