diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/db/test_datasets.py | 109 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 20 |
2 files changed, 57 insertions, 72 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py index 34fe7f0..4f405cb 100644 --- a/tests/unit/db/test_datasets.py +++ b/tests/unit/db/test_datasets.py @@ -1,51 +1,56 @@ from unittest import mock, TestCase +from gn3.db.datasets import ( + retrieve_dataset_name, + retrieve_riset_fields, + retrieve_geno_riset_fields, + retrieve_publish_riset_fields, + retrieve_probeset_riset_fields) class TestDatasetsDBFunctions(TestCase): - def test_retrieve_trait_dataset_name(self): + def test_retrieve_dataset_name(self): """Test that the function is called correctly.""" - for trait_type, thresh, trait_dataset_name, columns, table in [ - ["ProbeSet", 9, "testName", + for trait_type, thresh, trait_name, dataset_name, columns, table in [ + ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName", "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], - ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName", - "GenoFreeze"], - ["Publish", 6, "publishTraitName", + ["Geno", 3, "genoTraitName", "genoDatasetName", + "Id, Name, FullName, ShortName", "GenoFreeze"], + ["Publish", 6, "publishTraitName", "publishDatasetName", "Id, Name, FullName, ShortName", "PublishFreeze"], - ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName", - "TempFreeze"]]: + ["Temp", 4, "tempTraitName", "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") + cursor.fetchone.return_value = {} self.assertEqual( - retrieve_trait_dataset_name( - trait_type, thresh, trait_dataset_name, db_mock), - ("testName", "testNameFull", "testNameShort", - "dataScale")) + retrieve_dataset_name( + trait_type, thresh, trait_name, dataset_name, db_mock), + {}) cursor.execute.assert_called_once_with( - "SELECT %(columns)s " - "FROM %(table)s " + "SELECT {cols} " + "FROM {table} " "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}) + "(Name = %(name)s " + "OR FullName = %(name)s " + "OR ShortName = %(name)s)".format( + table=table, cols=columns, ttype=trait_type), + {"threshold": thresh, "name": dataset_name}) - def test_set_probeset_riset_fields(self): + def test_retrieve_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", ()]]: + ["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) + retrieve_probeset_riset_fields(trait_name, db_mock), + expected) cursor.execute.assert_called_once_with( ( "SELECT InbredSet.Name, InbredSet.Id" @@ -55,54 +60,45 @@ class TestDatasetsDBFunctions(TestCase): " AND ProbeSetFreeze.Name = %(name)s"), {"name": trait_name}) - def test_set_riset_fields(self): + def test_retrieve_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}] - ]: + for trait_type, trait_name, dataset_info, expected in [ + ["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"}, + {"dataset_name": "pubDBName01", "riset": ""}], + ["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"}, + {"dataset_name": "prbDBName01", "riset": ""}], + ["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"}, + {"dataset_name": "genoDBName01", "riset": ""}], + ["Temp", "tempTraitName01", {}, {"riset": ""}], + ]: db_mock = mock.MagicMock() - with self.subTest(trait_info=trait_info, expected=expected): + with self.subTest( + trait_type=trait_type, trait_name=trait_name, + dataset_info=dataset_info): with db_mock.cursor() as cursor: cursor.execute.return_value = ("riset_name", 0) self.assertEqual( - set_riset_fields(trait_info, db_mock), expected) + retrieve_riset_fields( + trait_type, trait_name, dataset_info, db_mock), + expected) - def test_set_publish_riset_fields(self): + def test_retrieve_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", ()]]: + ["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) + retrieve_publish_riset_fields(trait_name, db_mock), + expected) cursor.execute.assert_called_once_with( ( "SELECT InbredSet.Name, InbredSet.Id" @@ -111,19 +107,20 @@ class TestDatasetsDBFunctions(TestCase): " AND PublishFreeze.Name = %(name)s"), {"name": trait_name}) - def test_set_geno_riset_fields(self): + def test_retrieve_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", ()]]: + ["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) + retrieve_geno_riset_fields(trait_name, db_mock), + expected) cursor.execute.assert_called_once_with( ( "SELECT InbredSet.Name, InbredSet.Id" diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 7d161bf..5f52c18 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -142,25 +142,13 @@ class TestTraitsDBFunctions(TestCase): """Test that information on traits is retrieved as appropriate.""" for trait_type, threshold, trait_fullname, expected in [ ["Publish", 9, "pubDb::PublishTraitName::pubCell", - {"haveinfo": 0, "homologeneid": None, "type": "Publish", - "confidential": 0, "db": {"dataset_name": "pubDb"}, - "trait_name": "PublishTraitName", "cellid": "pubCell", - "trait_fullname": "pubDb::PublishTraitName::pubCell"}], + {"haveinfo": 0}], ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", - {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet", - "trait_fullname": "prbDb::ProbeSetTraitName::prbCell", - "db": {"dataset_name": "prbDb"}, - "trait_name": "ProbeSetTraitName", "cellid": "prbCell"}], + {"haveinfo": 0}], ["Geno", 12, "genDb::GenoTraitName", - {"haveinfo": 0, "homologeneid": None, "type": "Geno", - "trait_fullname": "genDb::GenoTraitName", - "db": {"dataset_name": "genDb"}, - "trait_name": "GenoTraitName", "cellid": ""}], + {"haveinfo": 0}], ["Temp", 6, "tmpDb::TempTraitName", - {"haveinfo": 0, "homologeneid": None, "type": "Temp", - "trait_fullname": "tmpDb::TempTraitName", - "db": {"dataset_name": "tmpDb"}, - "trait_name": "TempTraitName", "cellid": ""}]]: + {"haveinfo": 0}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: |