coordSystemAdaptor.t

# Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

use strict;

use Test::More;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
use Test::Exception;

our $verbose = 1; #set to 1 to turn on debug printouts

my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );


#
# Test constructor
#

my $csa = $db->get_CoordSystemAdaptor();

ok($csa && $csa->isa('Bio::EnsEMBL::DBSQL::CoordSystemAdaptor'));


#
# Test fetch_by_name()
#

my $cs = $csa->fetch_by_name('chromosome');

ok($cs->name eq 'chromosome');
ok($cs->dbID());
ok($cs->version eq 'NCBI33');
ok(!$cs->is_top_level());
ok(!$cs->is_sequence_level());
ok($cs->is_default());


my $version = $csa->get_default_version();
is($version, "NCBI33", "Found the correct default version");

my @versions = @{ $csa->get_all_versions() };
is($versions[0], "NCBI33", "Found the first version");


#
#  Test fetch_all_by_name
#
my @cs_list = @{$csa->fetch_all_by_name('chromosome')};

ok(@cs_list == 1);

ok($cs_list[0]->equals($cs));



#
# Test fetch_by_dbID()
#
$cs = $csa->fetch_by_dbID(3);

ok($cs->name() eq 'clone');
ok($cs->version() eq '');



#
# Test fetch_top_level
#
$cs = $csa->fetch_top_level();

ok($cs->name eq 'toplevel');
ok($cs->is_top_level());
ok($cs->rank == 0);

#
# Test fetch_by_rank
#
$cs = $csa->fetch_by_rank(1);
ok($cs->name() eq 'chromosome' && $cs->rank() == 1);

$cs = $csa->fetch_by_rank(0);
ok($cs->name() eq 'toplevel' && $cs->rank() == 0);


#
# Test fetch_sequence_level
#
$cs = $csa->fetch_sequence_level();

ok($cs->name eq 'contig');
ok($cs->is_sequence_level());


#
# Test fetch_all
#
@cs_list = @{$csa->fetch_all()};
my $prev_cs;

#make sure that they are ordered by rank
foreach my $cs (@cs_list) {
  if($prev_cs) {
    ok($prev_cs->rank < $cs->rank);
  }
  $prev_cs = $cs;
}


#
# Test get_mapping_path
#

my $ctg_cs = $csa->fetch_by_name('contig');
my $chr_cs = $csa->fetch_by_name('chromosome');
my $cln_cs = $csa->fetch_by_name('clone');

my $path = $csa->get_mapping_path($ctg_cs, $chr_cs);

ok(@$path == 2 &&
   $path->[0]->name() eq 'chromosome' &&
   $path->[1]->name() eq 'contig');

$path = $csa->get_mapping_path($chr_cs, $cln_cs);


ok(@$path == 3 &&
   (($path->[0]->name eq 'chromosome' &&  #there are 2 equally valid paths
     $path->[1]->name eq 'contig' &&
     $path->[2]->name eq 'clone')
    ||
    ($path->[0]->name eq 'clone' &&
     $path->[1]->name eq 'contig' &&
     $path->[2]->name eq 'chromosome'))
   );

#
# Test store
#

$multi->save('core', 'coord_system');
$multi->save('core', 'meta');

$cs = Bio::EnsEMBL::CoordSystem->new
  (-NAME            => 'newsystem',
   -VERSION         => 'NCBI35',
   -DEFAULT         => 1,
   -SEQUENCE_LEVEL  => 0,
   -RANK            => 10);

$csa->store($cs);

ok($cs->adaptor == $csa);
ok($cs->dbID());

#now make sure we can retrieve this
$cs = $csa->fetch_by_name('newsystem', 'NCBI35');
ok($cs->name eq 'newsystem');
ok($cs->version eq 'NCBI35');
ok($cs->is_default);
ok(!$cs->is_sequence_level);
ok(!$cs->is_top_level);
ok($cs->rank() == 10);

my $sth = $db->dbc->prepare('SELECT attrib FROM coord_system ' .
                       'WHERE  name = ? and version = ?');
$sth->execute('newsystem', 'NCBI35');

my ($attrib) = $sth->fetchrow_array();
ok($attrib eq 'default_version');
$sth->finish();

#
# Test store_mapping_path
#

my $new_paths = $csa->store_mapping_path( $cs, $cln_cs );
is( @{$new_paths}, 1, "Stored one result");
is( $new_paths->[0], 'newsystem:NCBI35|clone', "It maps newsystem to clone" );

my $new_path = $csa->get_mapping_path( $cs, $cln_cs );
is( @{$new_path}, 2, "Stored two results");
is( $new_path->[0]->name, 'newsystem', "Assembled is newsystem" );
is( $new_path->[1]->name, 'clone', "Component is clone");

my $new_paths2 = $csa->store_mapping_path( $cs, $cln_cs );
is( @{$new_paths2}, 0, "No mapping path was added" ); # Should not update second time round

my $new_paths3 = $csa->store_multiple_mapping_path($cs, $ctg_cs);
is( @{$new_paths3}, 1, "Added a multiple mapping path");
is( $new_paths3->[0], "newsystem:NCBI35#contig", "Multiple mapping between newsystem and clone");

#
# Do some inserting of mock coord systems and 
# do version retrieval
#
my $newcs_two = Bio::EnsEMBL::CoordSystem->new(
  -NAME            => 'newsystem_number_two',
  -VERSION         => 'NCBI35',
  -DEFAULT         => 0,
  -SEQUENCE_LEVEL  => 0,
  -RANK            => 11
);
$csa->store($newcs_two);

dies_ok { $csa->fetch_all_by_version() } 'fetch_all_by_version should die if not given a version to check';
is_deeply($csa->fetch_all_by_version('NCBI35'), [ $cs, $newcs_two ], 'Checking version rank retrieval works');
is_deeply(
  $csa->fetch_all_by_version('NCBI33'), 
  [$csa->fetch_by_name('chromosome')], 
  'Retrieval by name should return the same as version for NCBI33');
is_deeply($csa->fetch_all_by_version('thisdoesnotexist'), [], 'Bogus coordinate system results in no results');

$multi->restore('core', 'coord_system');
$multi->restore('core', 'meta');

done_testing();