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authorMuriithi Frederick Muriuki2021-08-05 13:08:57 +0300
committerMuriithi Frederick Muriuki2021-08-05 13:08:57 +0300
commitf1876f8b9939a9b863dc88aab8d3fed3c16ad4e1 (patch)
treedb150944193a94019735986a5aed28f84abfce67 /tests/unit/db/test_datasets.py
parent76ba5296c66e131301a9fdb692c3b2623f3331ed (diff)
downloadgenenetwork3-f1876f8b9939a9b863dc88aab8d3fed3c16ad4e1.tar.gz
Reorganise the database code
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Reorganise the code to separate the datasets from the traits, and to more closely conform to the same flow as that in GN1
Diffstat (limited to 'tests/unit/db/test_datasets.py')
-rw-r--r--tests/unit/db/test_datasets.py133
1 files changed, 133 insertions, 0 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
new file mode 100644
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+++ b/tests/unit/db/test_datasets.py
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+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})