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

18 files changed, 48 insertions, 41 deletions

diff --git a/gn3/api/search.py b/gn3/api/search.py
index aa844ee..ada845d 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -147,12 +147,14 @@ def parse_position(spec: str) -> tuple[Maybe[int], Maybe[int]]:
         point = apply_si_suffix(spec)
         return Just(max(0, point - width)), Just(point + width)
 
+def to_megabases(val):
+    """Convert `val` to megabases."""
+    return str(Decimal(val)/10**6)
 
 def parse_position_field(location_slot: int, query: bytes) -> xapian.Query:
     """Parse position and return a xapian query."""
     start, end = parse_position(query.decode("utf-8"))
     # TODO: Convert the xapian index to use bases instead of megabases.
-    to_megabases = lambda x: str(Decimal(x)/10**6)
     return (xapian.NumberRangeProcessor(location_slot)
             (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore
 
@@ -176,7 +178,6 @@ def parse_location_field(species_query: xapian.Query,
 
     def make_query(interval: ChromosomalInterval) -> xapian.Query:
         # TODO: Convert the xapian index to use bases instead of megabases.
-        to_megabases = lambda x: str(Decimal(x)/10**6)
         return combine_queries(xapian.Query.OP_AND,
                                species_query,
                                xapian.Query(chromosome_prefix + interval.chromosome),
diff --git a/gn3/auth/authentication/oauth2/endpoints/introspection.py b/gn3/auth/authentication/oauth2/endpoints/introspection.py
index a567363..29ade6a 100644
--- a/gn3/auth/authentication/oauth2/endpoints/introspection.py
+++ b/gn3/auth/authentication/oauth2/endpoints/introspection.py
@@ -24,7 +24,7 @@ class IntrospectionEndpoint(_IntrospectionEndpoint):
         """Query the token."""
         return _query_token(self, token_string, token_type_hint)
 
-    def introspect_token(self, token: OAuth2Token) -> dict:# pylint: disable=[no-self-use]
+    def introspect_token(self, token: OAuth2Token) -> dict:
         """Return the introspection information."""
         url = urlparse(flask_request.url)
         return {
@@ -43,6 +43,6 @@ class IntrospectionEndpoint(_IntrospectionEndpoint):
             "jti": token.token_id
         }
 
-    def check_permission(self, token, client, request):# pylint: disable=[unused-argument, no-self-use]
+    def check_permission(self, token, client, request):# pylint: disable=[unused-argument]
         """Check that the client has permission to introspect token."""
         return client.client_type == "internal"
diff --git a/gn3/auth/authentication/oauth2/endpoints/utilities.py b/gn3/auth/authentication/oauth2/endpoints/utilities.py
index 299f151..b85940d 100644
--- a/gn3/auth/authentication/oauth2/endpoints/utilities.py
+++ b/gn3/auth/authentication/oauth2/endpoints/utilities.py
@@ -12,7 +12,9 @@ def query_token(# pylint: disable=[unused-argument]
         endpoint_object: Any, token_str: str, token_type_hint) -> Optional[
             OAuth2Token]:
     """Retrieve the token from the database."""
-    __identity__ = lambda val: val
+    def __identity__(val):
+        """Identity function."""
+        return val
     token = Nothing
     with db.connection(current_app.config["AUTH_DB"]) as conn:
         if token_type_hint == "access_token":
diff --git a/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py b/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
index f80d02e..fb8d436 100644
--- a/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
+++ b/gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
@@ -41,7 +41,7 @@ class AuthorisationCodeGrant(grants.AuthorizationCodeGrant):
         """Retrieve the code from the database."""
         return __query_authorization_code__(code, client)
 
-    def delete_authorization_code(self, authorization_code):# pylint: disable=[no-self-use]
+    def delete_authorization_code(self, authorization_code):
         """Delete the authorisation code."""
         with db.connection(app.config["AUTH_DB"]) as conn:
             with db.cursor(conn) as cursor:
diff --git a/gn3/auth/authentication/oauth2/models/oauth2token.py b/gn3/auth/authentication/oauth2/models/oauth2token.py
index 72e20cc..981e730 100644
--- a/gn3/auth/authentication/oauth2/models/oauth2token.py
+++ b/gn3/auth/authentication/oauth2/models/oauth2token.py
@@ -51,7 +51,9 @@ class OAuth2Token(NamedTuple):
         return self.revoked
 
 def __token_from_resultset__(conn: db.DbConnection, rset) -> Maybe:
-    __identity__ = lambda val: val
+    def __identity__(val):
+        """Identity function."""
+        return val
     try:
         the_user = user_by_id(conn, uuid.UUID(rset["user_id"]))
     except NotFoundError as _nfe:
diff --git a/gn3/auth/db.py b/gn3/auth/db.py
index 2ba6619..97f3982 100644
--- a/gn3/auth/db.py
+++ b/gn3/auth/db.py
@@ -10,40 +10,32 @@ class DbConnection(Protocol):
     """Type annotation for a generic database connection object."""
     def cursor(self) -> Any:
         """A cursor object"""
-        ...
 
     def commit(self) -> Any:
         """Commit the transaction."""
-        ...
 
     def rollback(self) -> Any:
         """Rollback the transaction."""
-        ...
 
 class DbCursor(Protocol):
     """Type annotation for a generic database cursor object."""
     def execute(self, *args, **kwargs) -> Any:
         """Execute a single query"""
-        ...
 
     def executemany(self, *args, **kwargs) -> Any:
         """
         Execute parameterized SQL statement sql against all parameter sequences
         or mappings found in the sequence parameters.
         """
-        ...
 
     def fetchone(self, *args, **kwargs):
         """Fetch single result if present, or `None`."""
-        ...
 
     def fetchmany(self, *args, **kwargs):
         """Fetch many results if present or `None`."""
-        ...
 
     def fetchall(self, *args, **kwargs):
         """Fetch all results if present or `None`."""
-        ...
 
 @contextlib.contextmanager
 def connection(db_path: str, row_factory: Callable = sqlite3.Row) -> Iterator[DbConnection]:
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 9f02ad2..192ad7f 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -421,9 +421,8 @@ def literature_correlation_by_list(
     `web.webqtl.correlation.CorrelationPage.getLiteratureCorrelationByList`
     function in GeneNetwork1.
     """
-    if any((lambda t: (
-            bool(t.get("tissue_corr")) and
-            bool(t.get("tissue_p_value"))))(trait)
+    if any((bool(trait.get("tissue_corr")) and
+            bool(trait.get("tissue_p_value")))
            for trait in trait_list):
         temporary_table_name = f"LITERATURE{random_string(8)}"
         query1 = (
@@ -491,7 +490,7 @@ def tissue_correlation_by_list(
             "tissue_p_value": result["p-val"]
         }
 
-    if any((lambda t: bool(t.get("l_corr")))(trait) for trait in trait_list):
+    if any(bool((trait)) for trait in trait_list):
         prim_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
             (primary_trait_symbol,), tissue_probeset_freeze_id, conn)
         if primary_trait_symbol.lower() in prim_trait_symbol_value_dict:
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py
index 1d82f00..0794c0b 100644
--- a/gn3/db/case_attributes.py
+++ b/gn3/db/case_attributes.py
@@ -90,7 +90,8 @@ def approve_case_attribute(conn: Any, case_attr_audit_id: int) -> int:
                 elif diff_data.get("Deletion"):
                     data = diff_data.get("Deletion")
                     cursor.execute(
-                        "DELETE FROM CaseAttribute " "WHERE Id = %s",
+                        "DELETE FROM CaseAttribute "
+                        "WHERE Id = %s",
                         (data.get("id"),),
                     )
                 # Modification
diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 7d6a445..8bf7be7 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -21,7 +21,6 @@ class Connection(Protocol):
     """Type Annotation for MySQLdb's connection object"""
     def cursor(self, *args) -> Any:
         """A cursor in which queries may be performed"""
-        ...
 
 
 @contextlib.contextmanager
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.
         """