Retrieve trait information

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/db/traits.py: add functions to retrieve traits information
* tests/unit/db/test_traits.py: add tests for new function

  Add functions to retrieve traits information as is done in genenetwork1
  https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456

  At this point, the data retrieval functions are probably incomplete, as
  there is more of the `retrieveInfo` function in GN1 that has not been
  considered as of this commit.

1 files changed, 86 insertions, 6 deletions

diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 95c5b27..e3c5c28 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,13 +1,24 @@
 """Tests for gn3/db/traits.py"""
 from unittest import mock, TestCase
-from gn3.db.traits import retrieve_type_trait_name
+from gn3.db.traits import (
+    GENO_TRAIT_INFO_QUERY,
+    TEMP_TRAIT_INFO_QUERY,
+    PUBLISH_TRAIT_INFO_QUERY,
+    PROBESET_TRAIT_INFO_QUERY)
+from gn3.db.traits import (
+    retrieve_trait_info,
+    retrieve_geno_trait_info,
+    retrieve_temp_trait_info,
+    retrieve_trait_dataset_name,
+    retrieve_publish_trait_info,
+    retrieve_probeset_trait_info)
 
 class TestTraitsDBFunctions(TestCase):
     "Test cases for traits functions"
 
-    def test_retrieve_probeset_trait_name(self):
+    def test_retrieve_trait_dataset_name(self):
         """Test that the function is called correctly."""
-        for trait_type, thresh, trait_name, columns in [
+        for trait_type, thresh, trait_dataset_name, columns in [
                 ["ProbeSet", 9, "testName",
                  "Id, Name, FullName, ShortName, DataScale"],
                 ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"],
@@ -21,8 +32,8 @@ class TestTraitsDBFunctions(TestCase):
                         "testName", "testNameFull", "testNameShort",
                         "dataScale")
                     self.assertEqual(
-                        retrieve_type_trait_name(
-                            trait_type, thresh, trait_name, db_mock),
+                        retrieve_trait_dataset_name(
+                            trait_type, thresh, trait_dataset_name, db_mock),
                         ("testName", "testNameFull", "testNameShort",
                          "dataScale"))
                     cursor.execute.assert_called_once_with(
@@ -31,4 +42,73 @@ class TestTraitsDBFunctions(TestCase):
                         "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_name})
+                        {"threshold": thresh, "name": trait_dataset_name})
+
+    def test_retrieve_publish_trait_info(self):
+        """Test retrieval of type `Publish` traits."""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = tuple()
+            trait_source = {
+                "trait_name": "PublishTraitName", "trait_dataset_id": 1}
+            self.assertEqual(
+                retrieve_publish_trait_info(
+                    trait_source,
+                    db_mock),
+                tuple())
+            cursor.execute.assert_called_once_with(
+                PUBLISH_TRAIT_INFO_QUERY, trait_source)
+
+    def test_retrieve_probeset_trait_info(self):
+        """Test retrieval of type `Probeset` traits."""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = tuple()
+            trait_source = {
+                "trait_name": "ProbeSetTraitName",
+                "trait_dataset_name": "ProbeSetDatasetTraitName"}
+            self.assertEqual(
+                retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+            cursor.execute.assert_called_once_with(
+                PROBESET_TRAIT_INFO_QUERY, trait_source)
+
+    def test_retrieve_geno_trait_info(self):
+        """Test retrieval of type `Geno` traits."""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = tuple()
+            trait_source = {
+                "trait_name": "GenoTraitName",
+                "trait_dataset_name": "GenoDatasetTraitName"}
+            self.assertEqual(
+                retrieve_geno_trait_info(trait_source, db_mock), tuple())
+            cursor.execute.assert_called_once_with(
+                GENO_TRAIT_INFO_QUERY, trait_source)
+
+    def test_retrieve_temp_trait_info(self):
+        """Test retrieval of type `Temp` traits."""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = tuple()
+            trait_source = {"trait_name": "TempTraitName"}
+            self.assertEqual(
+                retrieve_temp_trait_info(trait_source, db_mock), tuple())
+            cursor.execute.assert_called_once_with(
+                TEMP_TRAIT_INFO_QUERY, trait_source)
+
+    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, in [
+                ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"],
+                ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"],
+                ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"],
+                ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]:
+            db_mock = mock.MagicMock()
+            with self.subTest(trait_type=trait_type):
+                with db_mock.cursor() as cursor:
+                    cursor.fetchone.return_value = tuple()
+                    self.assertEqual(
+                        retrieve_trait_info(
+                            trait_type, trait_name, trait_dataset_id,
+                            trait_dataset_name, db_mock),
+                        tuple())