# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: BioFetch_DB.t,v 1.13 2006/08/12 11:00:02 sendu Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
use lib '.','./blib/lib';
my $error;
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; };
    $error = 0;
    if( $@ ) {
        use lib 't';
    }
    use Test;
    $NUMTESTS = 27;
    plan tests => $NUMTESTS;
    eval { require IO::String; require LWP::UserAgent; 1; };
   if ( $@ ) {
      warn("No LWP::UserAgent or IO::String installed\n");
      $error = 1;
    }
}
END { 
    foreach ( $Test::ntest..$NUMTESTS) {
        skip('unable to run all of the Biblio/Biofetch tests - probably no network or LWP not installed',1);
    }
}
if( $error ==  1 ) {
    exit(0);
}
require Bio::DB::BioFetch;
my $verbose = -1;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run. 
my ($db,$db2,$seq,$seqio);
# get a single seq
$seq = $seqio = undef;
ok defined($db = new Bio::DB::BioFetch(-verbose => $verbose));
eval {
    # get a RefSeq entry
    ok $db->db('refseq');
    $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq VERSION
    $seq ? ok 1 : exit;
    ok $seq->accession_number;
    # EMBL
    $db->db('embl');
    ok(defined($seq = $db->get_Seq_by_acc('J00522')));
    ok( $seq->length, 408);
    ok(defined($seq = $db->get_Seq_by_acc('J02231')));
        ok $seq->id, 'J02231';
    ok( $seq->length, 200); 
    ok(defined($seqio = $db->get_Stream_by_id(['BUM'])));
    undef $db; # testing to see if we can remove gb
    ok( defined($seq = $seqio->next_seq()));
    ok( $seq->length, 200);
    #swissprot
    ok defined($db2 = new Bio::DB::BioFetch(-db => 'swissprot'));
    ok(defined($seq = $db2->get_Seq_by_id('YNB3_YEAST')));
    ok( $seq->length, 125);
    ok($seq->division, 'YEAST');
    $db2->request_format('fasta');
    ok(defined($seq = $db2->get_Seq_by_acc('P43780')));
    ok($seq->length,103); 
};
if ($@) {
    if( $DEBUG ) {
        print STDERR "Warning: Couldn't connect to EMBL with Bio::DB::EMBL.pm!\n" . $@;
    }
    foreach ( $Test::ntest..$NUMTESTS) { 
        skip('Could not open database, probably no network access',1);
    }
    exit(0);
}
$seq = $seqio = undef;
eval {
    $db = new Bio::DB::BioFetch(-retrievaltype => 'tempfile',
                                 -format => 'fasta',
                                 -verbose => $verbose
                                );
        $db->db('embl');
    ok( defined($seqio = $db->get_Stream_by_id('J00522 AF303112 J02231')));
    my %seqs;
    # don't assume anything about the order of the sequences
    while ( my $s = $seqio->next_seq ) {
        my ($type,$x,$name) = split(/\|/,$s->display_id);
        $seqs{$x} = $s->length;
    }
    ok($seqs{'J00522'},408);
    ok($seqs{'AF303112'},1611);
    ok($seqs{'J02231'},200);
};
if ($@) {
    if( $DEBUG ) { warn "Batch access test failed.\nError: $@\n"; }
    foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access skipping fasta retrieval',1); }
    exit(0);
}
$verbose = -1;
ok $db = new Bio::DB::BioFetch(-db => 'EMBL',
                               -verbose => $verbose);
eval {
    $seq = $db->get_Seq_by_acc('NT_006732');
};
ok $@;
eval {
    ok $seq = $db->get_Seq_by_acc('NM_006732');
    ok($seq );
    ok($seq->length, 3775);
};
if ($@) {
    if( $DEBUG ) { 
        print STDERR "Warning: Couldn't connect to BioFetch server with Bio::DB::BioFetch.pm!\n" . $@;
    }
    foreach ( $Test::ntest..$NUMTESTS) { 
        skip('Could not open database, probably no network access',1);
    }
    exit(0);
}