diff options
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_datasets.py | 133 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 196 |
2 files changed, 161 insertions, 168 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py new file mode 100644 index 0000000..34fe7f0 --- /dev/null +++ b/tests/unit/db/test_datasets.py @@ -0,0 +1,133 @@ +from unittest import mock, TestCase + +class TestDatasetsDBFunctions(TestCase): + + def test_retrieve_trait_dataset_name(self): + """Test that the function is called correctly.""" + for trait_type, thresh, trait_dataset_name, columns, table in [ + ["ProbeSet", 9, "testName", + "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], + ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName", + "GenoFreeze"], + ["Publish", 6, "publishTraitName", + "Id, Name, FullName, ShortName", "PublishFreeze"], + ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName", + "TempFreeze"]]: + db_mock = mock.MagicMock() + with self.subTest(trait_type=trait_type): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = ( + "testName", "testNameFull", "testNameShort", + "dataScale") + self.assertEqual( + retrieve_trait_dataset_name( + trait_type, thresh, trait_dataset_name, db_mock), + ("testName", "testNameFull", "testNameShort", + "dataScale")) + cursor.execute.assert_called_once_with( + "SELECT %(columns)s " + "FROM %(table)s " + "WHERE public > %(threshold)s AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( + cols=columns, ttype=trait_type), + {"threshold": thresh, "name": trait_dataset_name, + "table": table, "columns": columns}) + + def test_set_probeset_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'ProbeSet' trait type. + """ + for trait_name, expected in [ + ["testProbeSetName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_probeset_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, ProbeSetFreeze, ProbeFreeze" + " WHERE ProbeFreeze.InbredSetId = InbredSet.Id" + " AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId" + " AND ProbeSetFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_set_riset_fields(self): + """ + Test that the riset fields are set up correctly for the different trait + types. + """ + for trait_info, expected in [ + [{}, {}], + [{"haveinfo": 0, "type": "Publish"}, + {"haveinfo": 0, "type": "Publish"}], + [{"haveinfo": 0, "type": "ProbeSet"}, + {"haveinfo": 0, "type": "ProbeSet"}], + [{"haveinfo": 0, "type": "Geno"}, + {"haveinfo": 0, "type": "Geno"}], + [{"haveinfo": 0, "type": "Temp"}, + {"haveinfo": 0, "type": "Temp"}], + [{"haveinfo": 1, "type": "Publish", "name": "test"}, + {"haveinfo": 1, "type": "Publish", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "ProbeSet", "name": "test"}, + {"haveinfo": 1, "type": "ProbeSet", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Geno", "name": "test"}, + {"haveinfo": 1, "type": "Geno", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Temp", "name": "test"}, + {"haveinfo": 1, "type": "Temp", "name": "test", "riset": None, + "risetid": None}] + ]: + db_mock = mock.MagicMock() + with self.subTest(trait_info=trait_info, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = ("riset_name", 0) + self.assertEqual( + set_riset_fields(trait_info, db_mock), expected) + + def test_set_publish_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Publish' trait type. + """ + for trait_name, expected in [ + ["testPublishName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_publish_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, PublishFreeze" + " WHERE PublishFreeze.InbredSetId = InbredSet.Id" + " AND PublishFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_set_geno_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Geno' trait type. + """ + for trait_name, expected in [ + ["testGenoName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_geno_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, GenoFreeze" + " WHERE GenoFreeze.InbredSetId = InbredSet.Id" + " AND GenoFreeze.Name = %(name)s"), + {"name": trait_name}) diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 39d7a31..7d161bf 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -2,55 +2,19 @@ from unittest import mock, TestCase from gn3.db.traits import ( build_trait_name, - set_riset_fields, set_haveinfo_field, update_sample_data, retrieve_trait_info, - set_geno_riset_fields, set_confidential_field, set_homologene_id_field, retrieve_geno_trait_info, retrieve_temp_trait_info, - set_publish_riset_fields, - set_probeset_riset_fields, - retrieve_trait_dataset_name, retrieve_publish_trait_info, retrieve_probeset_trait_info) class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" - def test_retrieve_trait_dataset_name(self): - """Test that the function is called correctly.""" - for trait_type, thresh, trait_dataset_name, columns, table in [ - ["ProbeSet", 9, "testName", - "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], - ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName", - "GenoFreeze"], - ["Publish", 6, "publishTraitName", - "Id, Name, FullName, ShortName", "PublishFreeze"], - ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName", - "TempFreeze"]]: - db_mock = mock.MagicMock() - with self.subTest(trait_type=trait_type): - with db_mock.cursor() as cursor: - cursor.fetchone.return_value = ( - "testName", "testNameFull", "testNameShort", - "dataScale") - self.assertEqual( - retrieve_trait_dataset_name( - trait_type, thresh, trait_dataset_name, db_mock), - ("testName", "testNameFull", "testNameShort", - "dataScale")) - cursor.execute.assert_called_once_with( - "SELECT %(columns)s " - "FROM %(table)s " - "WHERE public > %(threshold)s AND " - "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( - cols=columns, ttype=trait_type), - {"threshold": thresh, "name": trait_dataset_name, - "table": table, "columns": columns}) - def test_retrieve_publish_trait_info(self): """Test retrieval of type `Publish` traits.""" db_mock = mock.MagicMock() @@ -159,10 +123,10 @@ class TestTraitsDBFunctions(TestCase): def test_build_trait_name_with_good_fullnames(self): for fullname, expected in [ ["testdb::testname", - {"trait_db": "testdb", "trait_name": "testname", "cellid": "", - "trait_fullname": "testdb::testname"}], + {"db": {"dataset_name": "testdb"}, "trait_name": "testname", + "cellid": "", "trait_fullname": "testdb::testname"}], ["testdb::testname::testcell", - {"trait_db": "testdb", "trait_name": "testname", + {"db": {"dataset_name": "testdb"}, "trait_name": "testname", "cellid": "testcell", "trait_fullname": "testdb::testname::testcell"}]]: with self.subTest(fullname=fullname): @@ -176,26 +140,26 @@ class TestTraitsDBFunctions(TestCase): def test_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" - for trait_type, trait_name, trait_dataset_id, trait_dataset_name, expected in [ - ["Publish", "pubDb::PublishTraitName::pubCell", 1, - "PublishDatasetTraitName", + for trait_type, threshold, trait_fullname, expected in [ + ["Publish", 9, "pubDb::PublishTraitName::pubCell", {"haveinfo": 0, "homologeneid": None, "type": "Publish", - "confidential": 0, "trait_db": "pubDb", + "confidential": 0, "db": {"dataset_name": "pubDb"}, "trait_name": "PublishTraitName", "cellid": "pubCell", "trait_fullname": "pubDb::PublishTraitName::pubCell"}], - ["ProbeSet", "prbDb::ProbeSetTraitName::prbCell", 2, - "ProbeSetDatasetTraitName", + ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet", "trait_fullname": "prbDb::ProbeSetTraitName::prbCell", - "trait_db": "prbDb", "trait_name": "ProbeSetTraitName", - "cellid": "prbCell"}], - ["Geno", "genDb::GenoTraitName", 3, "GenoDatasetTraitName", + "db": {"dataset_name": "prbDb"}, + "trait_name": "ProbeSetTraitName", "cellid": "prbCell"}], + ["Geno", 12, "genDb::GenoTraitName", {"haveinfo": 0, "homologeneid": None, "type": "Geno", - "trait_fullname": "genDb::GenoTraitName", "trait_db": "genDb", + "trait_fullname": "genDb::GenoTraitName", + "db": {"dataset_name": "genDb"}, "trait_name": "GenoTraitName", "cellid": ""}], - ["Temp", "tmpDb::TempTraitName", 4, "TempDatasetTraitName", + ["Temp", 6, "tmpDb::TempTraitName", {"haveinfo": 0, "homologeneid": None, "type": "Temp", - "trait_fullname": "tmpDb::TempTraitName", "trait_db": "tmpDb", + "trait_fullname": "tmpDb::TempTraitName", + "db": {"dataset_name": "tmpDb"}, "trait_name": "TempTraitName", "cellid": ""}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): @@ -203,8 +167,7 @@ class TestTraitsDBFunctions(TestCase): cursor.fetchone.return_value = tuple() self.assertEqual( retrieve_trait_info( - trait_type, trait_name, trait_dataset_id, - trait_dataset_name, db_mock), + trait_type, threshold, trait_fullname, db_mock), expected) def test_update_sample_data(self): @@ -246,128 +209,25 @@ class TestTraitsDBFunctions(TestCase): def test_set_homologene_id_field(self): """Test that the `homologene_id` field is set up correctly""" - for trait_info, expected in [ - [{"type": "Publish"}, - {"type": "Publish", "homologeneid": None}], - [{"type": "ProbeSet"}, - {"type": "ProbeSet", "homologeneid": None}], - [{"type": "Geno"}, {"type": "Geno", "homologeneid": None}], - [{"type": "Temp"}, {"type": "Temp", "homologeneid": None}]]: + for trait_type, trait_info, expected in [ + ["Publish", {}, {"homologeneid": None}], + ["ProbeSet", {}, {"homologeneid": None}], + ["Geno", {}, {"homologeneid": None}], + ["Temp", {}, {"homologeneid": None}]]: db_mock = mock.MagicMock() with self.subTest(trait_info=trait_info, expected=expected): with db_mock.cursor() as cursor: cursor.fetchone.return_value = () self.assertEqual( - set_homologene_id_field(trait_info, db_mock), expected) + set_homologene_id_field(trait_type, trait_info, db_mock), expected) def test_set_confidential_field(self): """Test that the `confidential` field is set up correctly""" - for trait_info, expected in [ - [{"type": "Publish"}, {"type": "Publish", "confidential": 0}], - [{"type": "ProbeSet"}, {"type": "ProbeSet"}], - [{"type": "Geno"}, {"type": "Geno"}], - [{"type": "Temp"}, {"type": "Temp"}]]: + for trait_type, trait_info, expected in [ + ["Publish", {}, {"confidential": 0}], + ["ProbeSet", {}, {}], + ["Geno", {}, {}], + ["Temp", {}, {}]]: with self.subTest(trait_info=trait_info, expected=expected): self.assertEqual( - set_confidential_field(trait_info), expected) - - def test_set_geno_riset_fields(self): - """ - Test that the `riset` and `riset_id` fields are retrieved appropriately - for the 'Geno' trait type. - """ - for trait_name, expected in [ - ["testGenoName", ()]]: - db_mock = mock.MagicMock() - with self.subTest(trait_name=trait_name, expected=expected): - with db_mock.cursor() as cursor: - cursor.execute.return_value = () - self.assertEqual( - set_geno_riset_fields(trait_name, db_mock), expected) - cursor.execute.assert_called_once_with( - ( - "SELECT InbredSet.Name, InbredSet.Id" - " FROM InbredSet, GenoFreeze" - " WHERE GenoFreeze.InbredSetId = InbredSet.Id" - " AND GenoFreeze.Name = %(name)s"), - {"name": trait_name}) - - - def test_set_publish_riset_fields(self): - """ - Test that the `riset` and `riset_id` fields are retrieved appropriately - for the 'Publish' trait type. - """ - for trait_name, expected in [ - ["testPublishName", ()]]: - db_mock = mock.MagicMock() - with self.subTest(trait_name=trait_name, expected=expected): - with db_mock.cursor() as cursor: - cursor.execute.return_value = () - self.assertEqual( - set_publish_riset_fields(trait_name, db_mock), expected) - cursor.execute.assert_called_once_with( - ( - "SELECT InbredSet.Name, InbredSet.Id" - " FROM InbredSet, PublishFreeze" - " WHERE PublishFreeze.InbredSetId = InbredSet.Id" - " AND PublishFreeze.Name = %(name)s"), - {"name": trait_name}) - - - def test_set_probeset_riset_fields(self): - """ - Test that the `riset` and `riset_id` fields are retrieved appropriately - for the 'ProbeSet' trait type. - """ - for trait_name, expected in [ - ["testProbeSetName", ()]]: - db_mock = mock.MagicMock() - with self.subTest(trait_name=trait_name, expected=expected): - with db_mock.cursor() as cursor: - cursor.execute.return_value = () - self.assertEqual( - set_probeset_riset_fields(trait_name, db_mock), expected) - cursor.execute.assert_called_once_with( - ( - "SELECT InbredSet.Name, InbredSet.Id" - " FROM InbredSet, ProbeSetFreeze, ProbeFreeze" - " WHERE ProbeFreeze.InbredSetId = InbredSet.Id" - " AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId" - " AND ProbeSetFreeze.Name = %(name)s"), - {"name": trait_name}) - - def test_set_riset_fields(self): - """ - Test that the riset fields are set up correctly for the different trait - types. - """ - for trait_info, expected in [ - [{}, {}], - [{"haveinfo": 0, "type": "Publish"}, - {"haveinfo": 0, "type": "Publish"}], - [{"haveinfo": 0, "type": "ProbeSet"}, - {"haveinfo": 0, "type": "ProbeSet"}], - [{"haveinfo": 0, "type": "Geno"}, - {"haveinfo": 0, "type": "Geno"}], - [{"haveinfo": 0, "type": "Temp"}, - {"haveinfo": 0, "type": "Temp"}], - [{"haveinfo": 1, "type": "Publish", "name": "test"}, - {"haveinfo": 1, "type": "Publish", "name": "test", - "riset": "riset_name", "risetid": 0}], - [{"haveinfo": 1, "type": "ProbeSet", "name": "test"}, - {"haveinfo": 1, "type": "ProbeSet", "name": "test", - "riset": "riset_name", "risetid": 0}], - [{"haveinfo": 1, "type": "Geno", "name": "test"}, - {"haveinfo": 1, "type": "Geno", "name": "test", - "riset": "riset_name", "risetid": 0}], - [{"haveinfo": 1, "type": "Temp", "name": "test"}, - {"haveinfo": 1, "type": "Temp", "name": "test", "riset": None, - "risetid": None}] - ]: - db_mock = mock.MagicMock() - with self.subTest(trait_info=trait_info, expected=expected): - with db_mock.cursor() as cursor: - cursor.execute.return_value = ("riset_name", 0) - self.assertEqual( - set_riset_fields(trait_info, db_mock), expected) + set_confidential_field(trait_type, trait_info), expected) |