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

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
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})