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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| # Copyright [2018-2019] 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 warnings; | ||
|
|
||
| use Bio::EnsEMBL::DataCheck::DbCheck; | ||
| use Bio::EnsEMBL::Test::MultiTestDB; | ||
|
|
||
| use FindBin; FindBin::again(); | ||
| use Path::Tiny; | ||
| use Test::Exception; | ||
| use Test::More; | ||
|
|
||
| use lib "$FindBin::Bin/TestChecks"; | ||
| use DbCheck_1; | ||
| use DbCheck_2; | ||
| use DbCheck_3; | ||
| use DbCheck_4; | ||
| use DbCheck_5; | ||
|
|
||
| my $test_db_dir = $FindBin::Bin; | ||
| my $dba_type = 'Bio::EnsEMBL::DBSQL::DBAdaptor'; | ||
|
|
||
| my $species = 'drosophila_melanogaster'; | ||
| my $db_type = 'core'; | ||
| my $testdb = Bio::EnsEMBL::Test::MultiTestDB->new($species, $test_db_dir); | ||
|
|
||
| my $dba = $testdb->get_DBAdaptor($db_type); | ||
|
|
||
| # Note that you cannot, by design, create a DbCheck object; datachecks | ||
| # must inherit from it and define mandatory, read-only parameters that | ||
| # are specific to that particular datacheck. So there's a limited amount | ||
| # of testing that we can do on the base class, the functionality is | ||
| # tested on a subclass. | ||
|
|
||
| my $module = 'Bio::EnsEMBL::DataCheck::DbCheck'; | ||
|
|
||
| subtest 'Fetch old DBA', sub { | ||
| # Getting a proper 'old' server is a pain, | ||
| # we just pretend that the test server is it. | ||
| my %conf = %{$$testdb{conf}{$db_type}}; | ||
| my $driver = $conf{driver}; | ||
| my $host = $conf{host}; | ||
| my $port = $conf{port}; | ||
| my $user = $conf{user}; | ||
| my $pass = $conf{pass}; | ||
|
|
||
| my $server_uri = "$driver://$user:$pass\@$host:$port/"; | ||
|
|
||
| # Need a test metadata db for retrieving the name of | ||
| # a previous release's database. | ||
| my $multi = Bio::EnsEMBL::Test::MultiTestDB->new('multi', $test_db_dir); | ||
| my $metadata_dba = $multi->get_DBAdaptor('metadata'); | ||
|
|
||
| my $check = TestChecks::DbCheck_1->new( | ||
| dba => $dba, | ||
| server_uri => $server_uri, | ||
| old_server_uri => $server_uri.$dba->dbc->dbname, | ||
| ); | ||
|
|
||
| # The test databases are added to the registry via MultiTestDB; but | ||
| # the datacheck code removes them as part of it's standard monkeying | ||
| # around, and their names are such that they are not picked up when | ||
| # the registry is subsequently loaded. So, we need to pre-load the | ||
| # registry, then add the metadata DBA back. | ||
| $check->load_registry(); | ||
| $check->registry->add_DBAdaptor('multi', 'metadata', $metadata_dba); | ||
|
|
||
| my $old_dba = $check->get_old_dba(); | ||
|
|
||
| isa_ok($old_dba, $dba_type, 'Return value of "get_old_dba"'); | ||
| is($old_dba->species, "${species}_old", 'Species has "_old" suffix'); | ||
|
|
||
| $check = TestChecks::DbCheck_1->new( | ||
| dba => $dba, | ||
| server_uri => $server_uri, | ||
| ); | ||
| throws_ok( | ||
| sub { $check->get_old_dba }, | ||
| qr/Old server details must be set/, | ||
| 'Fail if old_server_uri is not set'); | ||
|
|
||
| $check = TestChecks::DbCheck_1->new( | ||
| dba => $dba, | ||
| server_uri => $server_uri, | ||
| old_server_uri => $server_uri, | ||
| ); | ||
|
|
||
| throws_ok( | ||
| sub { $check->get_old_dba }, | ||
| qr/No metadata database found in the registry/, | ||
| 'Fail if metadata database does not exist'); | ||
|
|
||
| $check = TestChecks::DbCheck_1->new( | ||
| dba => $dba, | ||
| server_uri => $server_uri, | ||
| old_server_uri => $server_uri.'rhubarb_and_custard', | ||
| ); | ||
|
|
||
| throws_ok( | ||
| sub { $check->get_old_dba }, | ||
| qr/Specified database does not exist/, | ||
| 'Fail if specified database does not exist'); | ||
|
|
||
| $check = TestChecks::DbCheck_1->new( | ||
| dba => $dba, | ||
| server_uri => $server_uri, | ||
| old_server_uri => $server_uri.'95', | ||
| ); | ||
|
|
||
| $check->load_registry(); | ||
| $check->registry->add_DBAdaptor('multi', 'metadata', $metadata_dba); | ||
|
|
||
| throws_ok( | ||
| sub { $check->get_old_dba }, | ||
| qr/Database in metadata database does not exist/, | ||
| 'Fail if database from metadata database does not exist (1/2)'); | ||
|
|
||
| throws_ok( | ||
| sub { $check->get_old_dba('strigamia_maritima', 'core') }, | ||
| qr/Database in metadata database does not exist/, | ||
| 'Fail if database from metadata database does not exist (2/2)'); | ||
|
|
||
| $old_dba = $check->get_old_dba('dinanthropoides_nivalis', 'core'); | ||
| ok(! defined $old_dba, 'undef if no information in metadata database'); | ||
| }; | ||
|
|
||
| done_testing(); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| 1 95 \N 2019-01-01 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| 1 1 1 1 dmel_r6.17_FB2017_04 1 1 0 1 1 0 1 | ||
| 2 1 2 2 Ensembl Genomes v1.0 1 1 0 1 0 0 1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| 1 1 drosophila_melanogaster_core_95_6 1 core | ||
| 2 2 strigamia_maritima_core_42_95_1 1 core |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| 1 7227 0 7227 drosophila_melanogaster Drosophila_melanogaster Drosophila melanogaster Drosophila melanogaster \N \N \N \N | ||
| 2 126957 0 126957 strigamia_maritima Strigamia_maritima Strigamia maritima Strigamia maritima \N \N \N \N |
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