Fix linting errors caused by bump to Python 3.10migrate-to-python3.10

9 files changed, 31 insertions, 20 deletions

diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index d8c07f4..79ddaca 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -382,7 +382,7 @@ class GemmaAPITest(unittest.TestCase):
             "snps": "snpfile.txt",
         }
         mock_hash.return_value = "hash"
-        response = self.app.post(("/api/gemma/k-gwa-compute/" "my-token"))
+        response = self.app.post(("/api/gemma/k-gwa-compute/my-token"))
         mock_hash.assert_called_with([
             ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/'
              'genotype.txt'), '/tmp/my-token/phenofile.txt',
diff --git a/tests/unit/auth/test_groups.py b/tests/unit/auth/test_groups.py
index 4824e14..bd62405 100644
--- a/tests/unit/auth/test_groups.py
+++ b/tests/unit/auth/test_groups.py
@@ -19,7 +19,9 @@ create_group_failure = {
     "message": "Unauthorised: Failed to create group."
 }
 
-uuid_fn = lambda : UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
+def uuid_fn():
+    """Return a specific UUID"""
+    return UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
 
 GROUP = Group(UUID("9988c21d-f02f-4d45-8966-22c968ac2fbf"), "TheTestGroup",
               {"group_description": "The test group"})
diff --git a/tests/unit/auth/test_privileges.py b/tests/unit/auth/test_privileges.py
index 8395293..4894dfc 100644
--- a/tests/unit/auth/test_privileges.py
+++ b/tests/unit/auth/test_privileges.py
@@ -6,7 +6,9 @@ from gn3.auth.authorisation.privileges import Privilege, user_privileges
 
 from tests.unit.auth import conftest
 
-SORT_KEY = lambda x: x.privilege_id
+def sort_key(priv):
+    """Return the key to sort by"""
+    return priv.privilege_id
 
 PRIVILEGES = sorted(
     (Privilege("system:group:create-group", "Create a group"),
@@ -29,7 +31,7 @@ PRIVILEGES = sorted(
      Privilege("group:role:edit-role", "edit/update an existing role"),
      Privilege("group:user:assign-role", "Assign a role to an existing user"),
      Privilege("group:role:delete-role", "Delete an existing role")),
-    key=SORT_KEY)
+    key=sort_key)
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
@@ -43,4 +45,4 @@ def test_user_privileges(auth_testdb_path, fxtr_users, user, expected):# pylint:
     """
     with db.connection(auth_testdb_path) as conn:
         assert sorted(
-            user_privileges(conn, user), key=SORT_KEY) == expected
+            user_privileges(conn, user), key=sort_key) == expected
diff --git a/tests/unit/auth/test_resources.py b/tests/unit/auth/test_resources.py
index 2884add..a16dcb1 100644
--- a/tests/unit/auth/test_resources.py
+++ b/tests/unit/auth/test_resources.py
@@ -21,7 +21,9 @@ create_resource_failure = {
     "status": "error",
     "message": "Unauthorised: Could not create resource"
 }
-uuid_fn = lambda : uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
+def uuid_fn():
+    """UUID function for tests."""
+    return uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
@@ -71,7 +73,9 @@ def test_create_resource_raises_for_unauthorised_users(
         assert create_resource(
             conn, "test_resource", resource_category, user, False) == expected
 
-SORTKEY = lambda resource: resource.resource_id
+def sort_key(resource):
+    """Return the sort key for resources."""
+    return resource.resource_id
 
 @pytest.mark.unit_test
 def test_public_resources(fxtr_resources):
@@ -81,12 +85,12 @@ def test_public_resources(fxtr_resources):
     THEN: only list the resources that are public
     """
     conn, _res = fxtr_resources
-    assert sorted(public_resources(conn), key=SORTKEY) == sorted(tuple(
-        res for res in conftest.TEST_RESOURCES if res.public), key=SORTKEY)
+    assert sorted(public_resources(conn), key=sort_key) == sorted(tuple(
+        res for res in conftest.TEST_RESOURCES if res.public), key=sort_key)
 
 PUBLIC_RESOURCES = sorted(
     {res.resource_id: res for res in conftest.TEST_RESOURCES_PUBLIC}.values(),
-    key=SORTKEY)
+    key=sort_key)
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
@@ -97,13 +101,13 @@ PUBLIC_RESOURCES = sorted(
             {res.resource_id: res for res in
              (conftest.TEST_RESOURCES_GROUP_01 +
               conftest.TEST_RESOURCES_PUBLIC)}.values(),
-            key=SORTKEY),
+            key=sort_key),
          sorted(
              {res.resource_id: res for res in
               ((conftest.TEST_RESOURCES_GROUP_01[1],) +
                conftest.TEST_RESOURCES_PUBLIC)}.values()
              ,
-             key=SORTKEY),
+             key=sort_key),
          PUBLIC_RESOURCES, PUBLIC_RESOURCES))))
 def test_user_resources(fxtr_group_user_roles, user, expected):
     """
@@ -114,4 +118,4 @@ def test_user_resources(fxtr_group_user_roles, user, expected):
     conn, *_others = fxtr_group_user_roles
     assert sorted(
         {res.resource_id: res for res in user_resources(conn, user)
-         }.values(), key=SORTKEY) == expected
+         }.values(), key=sort_key) == expected
diff --git a/tests/unit/auth/test_roles.py b/tests/unit/auth/test_roles.py
index 02fd9f7..3bb84a3 100644
--- a/tests/unit/auth/test_roles.py
+++ b/tests/unit/auth/test_roles.py
@@ -16,7 +16,9 @@ create_role_failure = {
     "message": "Unauthorised: Could not create role"
 }
 
-uuid_fn = lambda : uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
+def uuid_fn():
+    """UUID function for tests"""
+    return uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b")
 
 PRIVILEGES = (
     Privilege("group:resource:view-resource",
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py
index 20cd6bc..066c650 100644
--- a/tests/unit/computations/test_partial_correlations.py
+++ b/tests/unit/computations/test_partial_correlations.py
@@ -234,7 +234,7 @@ class TestPartialCorrelations(TestCase):
                     tissue_correlation(primary, target, method)
 
     @pytest.mark.unit_test
-    def test_tissue_correlation(self): # pylint: disable=R0201
+    def test_tissue_correlation(self):
         """
         Test that the correct correlation values are computed for the given:
         - primary trait
diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py
index 175249b..596f78a 100644
--- a/tests/unit/db/test_case_attributes.py
+++ b/tests/unit/db/test_case_attributes.py
@@ -140,7 +140,7 @@ def test_approve_deleting_case_attribute(mocker: MockFixture) -> None:
                 "WHERE id = %s",
                 (3,),
             ),
-            mocker.call("DELETE FROM CaseAttribute " "WHERE Id = %s", ("12",)),
+            mocker.call("DELETE FROM CaseAttribute WHERE Id = %s", ("12",)),
             mocker.call(
                 "UPDATE caseattributes_audit SET "
                 "status = 'approved' WHERE id = %s",
@@ -183,14 +183,16 @@ def test_approve_modifying_case_attribute(mocker: MockFixture) -> None:
                 (3,),
             ),
             mocker.call(
-                "UPDATE CaseAttribute SET " "Description = %s WHERE Id = %s",
+                "UPDATE CaseAttribute SET "
+                "Description = %s WHERE Id = %s",
                 (
                     "Test",
                     "12",
                 ),
             ),
             mocker.call(
-                "UPDATE CaseAttribute SET " "Name = %s WHERE Id = %s",
+                "UPDATE CaseAttribute SET "
+                "Name = %s WHERE Id = %s",
                 (
                     "Height (A)",
                     "12",
diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py
index 8ac468c..2b4151c 100644
--- a/tests/unit/db/test_db.py
+++ b/tests/unit/db/test_db.py
@@ -103,7 +103,6 @@ class TestCrudMethods(TestCase):
                 (35, 'Rob'))
 
     @pytest.mark.unit_test
-    # pylint: disable=R0201
     def test_probeset_called_with_right_columns(self):
         """Given a columns argument, test that the correct sql query is
         constructed"""
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index 8781d6f..3d4fc78 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -29,7 +29,7 @@ class TestHeatmap(TestCase):
     """Class for testing heatmap computation functions"""
 
     @pytest.mark.unit_test
-    def test_cluster_traits(self): # pylint: disable=R0201
+    def test_cluster_traits(self):
         """
         Test that the clustering is working as expected.
         """