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use lib 't';
use strict;
use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 9;
}
use MultiTestDB;
use TestUtils qw ( debug test_getter_setter );
use Bio::EnsEMBL::DBEntry;
# switch on the debug prints
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debug( "Startup test" );
#
# 1 Test started
#
ok(1);
my $multi = MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
debug( "Test database instatiated" );
#
# 2 Database instatiated
#
ok( $db );
# some retrievals
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
my $sth = $db->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
$sth->execute();
my ( $xref_count ) = $sth->fetchrow_array();
my $db_entry_count = 0;
my $goxref_count = 0;
my $ident_count = 0;
$sth->finish();
my $ga = $db->get_GeneAdaptor();
my $all_gene_ids = $ga->list_geneIds();
for my $gene_id ( @$all_gene_ids ) {
my $gene = $ga->fetch_by_dbID( $gene_id );
for my $tr ( @{$gene->get_all_Transcripts()} ) {
my $tl = $tr->translation();
my $dbentries = $dbEntryAdaptor->fetch_all_by_Translation( $tl );
$db_entry_count += scalar( @{$dbentries});
$goxref_count += grep { $_->isa( "Bio::EnsEMBL::GoXref" )} @$dbentries;
$ident_count += grep {$_->isa( "Bio::EnsEMBL::IdentityXref" )} @$dbentries;
}
}
debug( "Found $xref_count xrefs and $db_entry_count dblinks." );
debug( " $goxref_count GoXrefs, $ident_count identityXrefs." );
#
# 3 as many dblinks as entries in object_xref
#
ok( $db_entry_count == $xref_count );
#
# 4,5 correct number of GoXrefs and IdentityXrefs
#
ok( $goxref_count == 48 );
ok( $ident_count == 32 );
# try storing and retrieval
my $xref = Bio::EnsEMBL::DBEntry->new
(
-primary_id => "1",
-dbname => "SWISSPROT",
-release => "1",
-display_id => "Ens related thing"
);
my %goxref = %$xref;
my %identxref = %$xref;
my $goref = Bio::EnsEMBL::GoXref->new
(
-primary_id => "1",
-dbname => "GO",
-release => "1",
-display_id => "Ens related GO"
);
$goref->linkage_type( "experimental" );
my $ident_xref = Bio::EnsEMBL::IdentityXref->new
(
-primary_id => "1",
-dbname => "SPTREMBL",
-release => "1",
-display_id => "Ens related Ident"
);
$ident_xref->query_identity( 100 );
$ident_xref->target_identity( 95 );
$multi->hide( "core", "object_xref", "xref", "identity_xref", "go_xref" );
my $gene = $ga->fetch_by_dbID( $all_gene_ids->[0] );
my $tr = $gene->get_all_Transcripts()->[0];
my $tl = $tr->translation();
$dbEntryAdaptor->store( $xref, $gene, "Gene" );
$dbEntryAdaptor->store( $xref, $tr, "Transcript" );
$dbEntryAdaptor->store( $goref, $tl, "Translation" );
$dbEntryAdaptor->store( $ident_xref, $tl, "Translation" );
$dbEntryAdaptor->store( $ident_xref, $tr, "Transcript" );
my ( $oxr_count, $go_count );
$sth = $db->prepare( "select count(*) from object_xref" );
$sth->execute();
( $oxr_count ) = $sth->fetchrow_array();
$sth->finish();
#
# 6 right number of object xrefs in db
#
debug( "object_xref_count = $oxr_count" );
ok( $oxr_count == 5 );
$sth = $db->prepare( "select count(*) from xref" );
$sth->execute();
( $xref_count ) = $sth->fetchrow_array();
$sth->finish();
#
# 7 number of xrefs right
#
debug( "Number of xrefs = $xref_count" );
ok( $xref_count == 3 );
$sth = $db->prepare( "select count(*) from go_xref" );
$sth->execute();
( $go_count ) = $sth->fetchrow_array();
$sth->finish();
#
# 8 number of go entries right
#
debug( "Number of go_xrefs = $go_count" );
ok( $go_count == 1 );
$sth = $db->prepare( "select count(*) from identity_xref" );
$sth->execute();
( $ident_count ) = $sth->fetchrow_array();
$sth->finish();
#
# 9 identity xrefs right
#
# the identity (query/target)values are not normalized ...
debug( "Number of identity_xrefs = $ident_count" );
ok( $ident_count == 2 );
#
# Need more tests here ...
#
$multi->restore();