# -*-Perl-*- Test Harness script for Bioperl
# $Id: BioFetch.t 16091 2009-09-15 22:11:15Z cjfields $

use strict;

BEGIN { 
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 36,
			   -requires_modules => [qw(IO::String LWP::UserAgent)],
			   -requires_networking => 1);
	
	use_ok('Bio::DB::BioFetch');
}

my $verbose = test_debug();

my $dbwarn = "Warning: Couldn't connect to EMBL with Bio::DB::BioFetch!\n";

my ($db,$db2,$seq,$seqio);

SKIP :{
	# get a single seq
	ok defined($db = Bio::DB::BioFetch->new(-verbose => $verbose));
	# get a RefSeq entry
	ok $db->db('refseq');
	eval {
		$seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq VERSION
	};
	skip($dbwarn, 4) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->accession_number,'NM_006732');
	is($seq->accession_number,'NM_006732');
	is( $seq->length, 3776);
}

SKIP: {
	# EMBL
	$db->db('embl');
	eval {
		$seq = $db->get_Seq_by_acc('J02231');    
	};
	skip($dbwarn, 3) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->id, 'J02231');
	is($seq->length, 200);
}

SKIP: {
	eval {
		$seqio = $db->get_Stream_by_id(['BUM']);
	};
	skip($dbwarn, 3) if $@;
	undef $db; # testing to see if we can remove gb
	$seq = $seqio->next_seq();
	isa_ok($seqio, 'Bio::SeqIO');
	isa_ok($seq, 'Bio::SeqI');
	cmp_ok( $seq->length, '>=', 1);
}

SKIP: {
	#swissprot
	ok $db2 = Bio::DB::BioFetch->new(-db => 'swissprot');
	eval {
		$seq = $db2->get_Seq_by_id('YNB3_YEAST');
	};
	skip($dbwarn, 5) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->length, 125);
	is($seq->division, 'YEAST');
	$db2->request_format('fasta');
	eval {
		$seq = $db2->get_Seq_by_acc('P43780');
	};
	skip($dbwarn, 2) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->length,103);
}

$seq = $seqio = undef;

SKIP: {
	ok $db = Bio::DB::BioFetch->new(-retrievaltype => 'tempfile',
					 -format => 'fasta',
					 -verbose => $verbose
					);
	$db->db('embl');
	eval {
		$seqio = $db->get_Stream_by_id('J00522 AF303112 J02231');
	};
	skip($dbwarn, 7) if $@;
	my %seqs;
	# don't assume anything about the order of the sequences
	while ( my $s = $seqio->next_seq ) {
		isa_ok($s, 'Bio::SeqI');
		my ($type,$x,$name) = split(/\|/,$s->display_id);
		$seqs{$x} = $s->length;
	}
	isa_ok($seqio, 'Bio::SeqIO');
	is($seqs{'J00522'},408);
	is($seqs{'AF303112'},1611);
	is($seqs{'J02231'},200);
}

SKIP: {
	ok $db = Bio::DB::BioFetch->new(-db => 'embl', -verbose => $verbose ? $verbose : -1);
	
	# check contig warning (WebDBSeqI)
	eval {
		$seq = $db->get_Seq_by_acc('NT_006732');
	};
	like($@, qr{contigs are whole chromosome files}, 'contig warning');
	eval {
		$seq = $db->get_Seq_by_acc('NM_006732');
	};
	skip($dbwarn, 3) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->length,3776);
}
    
# unisave
SKIP: {
	ok $db = Bio::DB::BioFetch->new(-db => 'unisave',
				   -verbose => $verbose);
	eval {
		$seq = $db->get_Seq_by_acc('LAM1_MOUSE');
	};
	skip($dbwarn, 3) if $@;
	isa_ok($seq, 'Bio::SeqI');
	is($seq->display_id, 'LAM1_MOUSE');
	is($seq->accession, 'P14733');   
	is($seq->length, 587);   
}