From 8bb89dd929506af37675ed5e65737ac79ca0678e Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:41:41 +0300 Subject: Fix C3001: Lambda expression assigned to a variable Signed-off-by: Munyoki Kilyungi --- gn3/api/search.py | 6 ++++-- .../authentication/oauth2/endpoints/utilities.py | 3 ++- .../authentication/oauth2/models/oauth2token.py | 3 ++- gn3/computations/partial_correlations.py | 6 ++---- gn3/db/partial_correlations.py | 3 +-- tests/unit/auth/test_groups.py | 5 ++++- tests/unit/auth/test_privileges.py | 5 ++--- tests/unit/auth/test_resources.py | 25 ++++++++++++++-------- tests/unit/auth/test_roles.py | 6 +++++- 9 files changed, 38 insertions(+), 24 deletions(-) diff --git a/gn3/api/search.py b/gn3/api/search.py index aa844ee..c741b15 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -152,7 +152,8 @@ 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) + def to_megabases(val): + return str(Decimal(val)/10**6) return (xapian.NumberRangeProcessor(location_slot) (start.maybe("", to_megabases), end.maybe("", to_megabases))) # type: ignore @@ -176,7 +177,8 @@ 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) + def to_megabases(val): + return str(Decimal(val)/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/utilities.py b/gn3/auth/authentication/oauth2/endpoints/utilities.py index 299f151..e13784e 100644 --- a/gn3/auth/authentication/oauth2/endpoints/utilities.py +++ b/gn3/auth/authentication/oauth2/endpoints/utilities.py @@ -12,7 +12,8 @@ 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): + 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/models/oauth2token.py b/gn3/auth/authentication/oauth2/models/oauth2token.py index 72e20cc..bfe4aaf 100644 --- a/gn3/auth/authentication/oauth2/models/oauth2token.py +++ b/gn3/auth/authentication/oauth2/models/oauth2token.py @@ -51,7 +51,8 @@ class OAuth2Token(NamedTuple): return self.revoked def __token_from_resultset__(conn: db.DbConnection, rset) -> Maybe: - __identity__ = lambda val: val + def __identity__(val): + return val try: the_user = user_by_id(conn, uuid.UUID(rset["user_id"])) except NotFoundError as _nfe: diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 9f02ad2..6eee299 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -421,9 +421,7 @@ 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 +489,7 @@ 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.get("l_corr")) 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/partial_correlations.py b/gn3/db/partial_correlations.py index e8466f6..1368da0 100644 --- a/gn3/db/partial_correlations.py +++ b/gn3/db/partial_correlations.py @@ -422,8 +422,7 @@ def set_bxd(group_info): return { **group_info, "group": ( - "BXD" if group_info.get("Name") == "BXD300" - else group_info.get("Name", "")), + "BXD" if group_info.get("Name") == "BXD300" else group_info.get("Name", "")), "groupid": group_info["Id"] } diff --git a/tests/unit/auth/test_groups.py b/tests/unit/auth/test_groups.py index 4824e14..d3b8fd4 100644 --- a/tests/unit/auth/test_groups.py +++ b/tests/unit/auth/test_groups.py @@ -19,7 +19,10 @@ create_group_failure = { "message": "Unauthorised: Failed to create group." } -uuid_fn = lambda : UUID("d32611e3-07fc-4564-b56c-786c6db6de2b") +def uuid_fn(): + """Mock function for 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..3c645c7 100644 --- a/tests/unit/auth/test_privileges.py +++ b/tests/unit/auth/test_privileges.py @@ -6,7 +6,6 @@ from gn3.auth.authorisation.privileges import Privilege, user_privileges from tests.unit.auth import conftest -SORT_KEY = lambda x: x.privilege_id PRIVILEGES = sorted( (Privilege("system:group:create-group", "Create a group"), @@ -29,7 +28,7 @@ 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=lambda x: x.privilege_id) @pytest.mark.unit_test @pytest.mark.parametrize( @@ -43,4 +42,4 @@ 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=lambda x: x.privilege_id) == expected diff --git a/tests/unit/auth/test_resources.py b/tests/unit/auth/test_resources.py index 2884add..7b9798a 100644 --- a/tests/unit/auth/test_resources.py +++ b/tests/unit/auth/test_resources.py @@ -21,7 +21,12 @@ create_resource_failure = { "status": "error", "message": "Unauthorised: Could not create resource" } -uuid_fn = lambda : uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b") + + +def uuid_fn(): + """Mock function for uuid""" + return uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b") + @pytest.mark.unit_test @pytest.mark.parametrize( @@ -71,7 +76,6 @@ 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 @pytest.mark.unit_test def test_public_resources(fxtr_resources): @@ -81,12 +85,16 @@ 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=lambda resource: resource.resource_id) == sorted(tuple( + res for res in + conftest.TEST_RESOURCES + if res.public), key=lambda resource: resource.resource_id) PUBLIC_RESOURCES = sorted( {res.resource_id: res for res in conftest.TEST_RESOURCES_PUBLIC}.values(), - key=SORTKEY) + key=lambda resource: resource.resource_id) @pytest.mark.unit_test @pytest.mark.parametrize( @@ -97,13 +105,12 @@ PUBLIC_RESOURCES = sorted( {res.resource_id: res for res in (conftest.TEST_RESOURCES_GROUP_01 + conftest.TEST_RESOURCES_PUBLIC)}.values(), - key=SORTKEY), + key=lambda resource: resource.resource_id), sorted( {res.resource_id: res for res in ((conftest.TEST_RESOURCES_GROUP_01[1],) + conftest.TEST_RESOURCES_PUBLIC)}.values() - , - key=SORTKEY), + , key=lambda resource: resource.resource_id), PUBLIC_RESOURCES, PUBLIC_RESOURCES)))) def test_user_resources(fxtr_group_user_roles, user, expected): """ @@ -114,4 +121,4 @@ 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=lambda resource: resource.resource_id) == expected diff --git a/tests/unit/auth/test_roles.py b/tests/unit/auth/test_roles.py index 02fd9f7..8e22bb5 100644 --- a/tests/unit/auth/test_roles.py +++ b/tests/unit/auth/test_roles.py @@ -16,7 +16,11 @@ create_role_failure = { "message": "Unauthorised: Could not create role" } -uuid_fn = lambda : uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b") + +def uuid_fn(): + """Mock function for uuid""" + return uuid.UUID("d32611e3-07fc-4564-b56c-786c6db6de2b") + PRIVILEGES = ( Privilege("group:resource:view-resource", -- cgit v1.2.3