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authorMuriithi Frederick Muriuki2021-07-28 12:32:43 +0300
committerBonfaceKilz2021-07-29 15:24:51 +0300
commit00579657abf5f9cadda1a9a479cae63ace28820c (patch)
treeac01a98f56742599988347271b0d786b2f53eb5c /tests/unit/db
parent8d7f8eec5b5d84937e453c9b02de0bd1b1727265 (diff)
downloadgenenetwork3-00579657abf5f9cadda1a9a479cae63ace28820c.tar.gz
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.
Diffstat (limited to 'tests/unit/db')
-rw-r--r--tests/unit/db/test_traits.py92
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())