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-rw-r--r--gn3/api/search.py2
-rw-r--r--migrations/auth/20221110_01_WtZ1I-create-resources-table.py3
-rw-r--r--migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py5
-rw-r--r--migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py5
-rw-r--r--migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py5
-rw-r--r--migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py1
-rw-r--r--mypy.ini3
-rw-r--r--tests/unit/auth/fixtures/group_fixtures.py51
-rw-r--r--tests/unit/auth/fixtures/resource_fixtures.py9
-rw-r--r--tests/unit/auth/test_groups.py7
-rw-r--r--tests/unit/auth/test_resources.py9
-rw-r--r--tests/unit/auth/test_roles.py3
-rw-r--r--tests/unit/auth/test_token.py9
13 files changed, 85 insertions, 27 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py
index 4ba2590..3cdee67 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -153,7 +153,7 @@ def apply_si_suffix(location: str) -> int:
return int(float(location[:-1])*10**suffixes.get(location[-1].lower(), 0))
-def parse_location_field(lifted_species: str, species_prefix: str,
+def parse_location_field(lifted_species: str, species_prefix: str, # pylint: disable=[too-many-arguments]
chromosome_prefix: str, location_slot: int,
liftover_function: IntervalLiftoverFunction,
query: bytes) -> xapian.Query:
diff --git a/migrations/auth/20221110_01_WtZ1I-create-resources-table.py b/migrations/auth/20221110_01_WtZ1I-create-resources-table.py
index f99d482..09ed891 100644
--- a/migrations/auth/20221110_01_WtZ1I-create-resources-table.py
+++ b/migrations/auth/20221110_01_WtZ1I-create-resources-table.py
@@ -11,9 +11,10 @@ steps = [
"""
CREATE TABLE IF NOT EXISTS resources(
group_id TEXT NOT NULL,
- resource_id TEXT PRIMARY KEY,
+ resource_id TEXT NOT NULL,
resource_name TEXT NOT NULL,
resource_category_id TEXT NOT NULL,
+ PRIMARY KEY(group_id, resource_id),
FOREIGN KEY(group_id) REFERENCES groups(group_id),
FOREIGN KEY(resource_category_id) REFERENCES resource_categories(resource_category_id)
) WITHOUT ROWID
diff --git a/migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py b/migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py
index 0959116..d3f97ac 100644
--- a/migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py
+++ b/migrations/auth/20221110_02_z1dWf-create-mrna-resources-table.py
@@ -13,9 +13,12 @@ steps = [
step(
"""
CREATE TABLE IF NOT EXISTS mrna_resources(
+ group_id TEXT NOT NULL,
resource_id TEXT PRIMARY KEY,
dataset_id TEXT NOT NULL UNIQUE,
- FOREIGN KEY(resource_id) REFERENCES resources(resource_id)
+ FOREIGN KEY(group_id, resource_id)
+ REFERENCES resources(group_id, resource_id)
+ ON UPDATE CASCADE ON DELETE RESTRICT
) WITHOUT ROWID
""",
"DROP TABLE IF EXISTS mrna_resources")
diff --git a/migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py b/migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py
index d241f77..7dde67e 100644
--- a/migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py
+++ b/migrations/auth/20221110_03_ka3W0-create-phenotype-resources-table.py
@@ -13,10 +13,13 @@ steps = [
step(
"""
CREATE TABLE IF NOT EXISTS phenotype_resources(
+ group_id TEXT NOT NULL,
resource_id TEXT NOT NULL,
trait_id TEXT NOT NULL UNIQUE,
PRIMARY KEY(resource_id, trait_id),
- FOREIGN KEY(resource_id) REFERENCES resources(resource_id)
+ FOREIGN KEY(group_id, resource_id)
+ REFERENCES resources(group_id, resource_id)
+ ON UPDATE CASCADE ON DELETE RESTRICT
) WITHOUT ROWID
""",
"DROP TABLE IF EXISTS phenotype_resources")
diff --git a/migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py b/migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py
index 9200774..ed6e87d 100644
--- a/migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py
+++ b/migrations/auth/20221110_04_6PRFQ-create-genotype-resources-table.py
@@ -13,10 +13,13 @@ steps = [
step(
"""
CREATE TABLE IF NOT EXISTS genotype_resources(
+ group_id TEXT NOT NULL,
resource_id TEXT NOT NULL,
trait_id TEXT NOT NULL UNIQUE,
PRIMARY KEY(resource_id, trait_id),
- FOREIGN KEY(resource_id) REFERENCES resources(resource_id)
+ FOREIGN KEY(group_id, resource_id)
+ REFERENCES resources(group_id, resource_id)
+ ON UPDATE CASCADE ON DELETE RESTRICT
) WITHOUT ROWID
""",
"DROP TABLE IF EXISTS genotype_resources")
diff --git a/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py b/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py
index 7115bc3..2deff10 100644
--- a/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py
+++ b/migrations/auth/20221117_01_RDlfx-modify-group-roles-add-group-role-id.py
@@ -33,6 +33,7 @@ steps = [
group_role_id TEXT PRIMARY KEY,
group_id TEXT NOT NULL,
role_id TEXT NOT NULL,
+ UNIQUE (group_id, role_id),
FOREIGN KEY(group_id) REFERENCES groups(group_id),
FOREIGN KEY(role_id) REFERENCES roles(role_id)
) WITHOUT ROWID
diff --git a/mypy.ini b/mypy.ini
index dfedb13..1fcf703 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -54,3 +54,6 @@ ignore_missing_imports = True
[mypy-authlib.*]
ignore_missing_imports = True
+
+[mypy-pymonad.*]
+ignore_missing_imports = True
diff --git a/tests/unit/auth/fixtures/group_fixtures.py b/tests/unit/auth/fixtures/group_fixtures.py
index 72b96d1..1830374 100644
--- a/tests/unit/auth/fixtures/group_fixtures.py
+++ b/tests/unit/auth/fixtures/group_fixtures.py
@@ -7,6 +7,8 @@ from gn3.auth import db
from gn3.auth.authorisation.groups import Group, GroupRole
from gn3.auth.authorisation.resources import Resource, ResourceCategory
+from .role_fixtures import RESOURCE_EDITOR_ROLE, RESOURCE_READER_ROLE
+
TEST_GROUP_01 = Group(uuid.UUID("9988c21d-f02f-4d45-8966-22c968ac2fbf"),
"TheTestGroup")
TEST_GROUP_02 = Group(uuid.UUID("e37d59d7-c05e-4d67-b479-81e627d8d634"),
@@ -45,6 +47,9 @@ TEST_RESOURCES_GROUP_02 = (
TEST_RESOURCES = TEST_RESOURCES_GROUP_01 + TEST_RESOURCES_GROUP_02
TEST_RESOURCES_PUBLIC = (TEST_RESOURCES_GROUP_01[0], TEST_RESOURCES_GROUP_02[1])
+def __gtuple__(cursor):
+ return tuple(dict(row) for row in cursor.fetchall())
+
@pytest.fixture(scope="function")
def fxtr_group(conn_after_auth_migrations):# pylint: disable=[redefined-outer-name]
"""Fixture: setup a test group."""
@@ -57,6 +62,11 @@ def fxtr_group(conn_after_auth_migrations):# pylint: disable=[redefined-outer-na
yield (conn_after_auth_migrations, TEST_GROUPS[0])
+ with db.cursor(conn_after_auth_migrations) as cursor:
+ cursor.executemany(
+ "DELETE FROM groups WHERE group_id=?",
+ ((str(group.group_id),) for group in TEST_GROUPS))
+
@pytest.fixture(scope="function")
def fxtr_users_in_group(fxtr_group, fxtr_users):# pylint: disable=[redefined-outer-name, unused-argument]
"""Link the users to the groups."""
@@ -78,9 +88,8 @@ def fxtr_users_in_group(fxtr_group, fxtr_users):# pylint: disable=[redefined-out
query_params)
@pytest.fixture(scope="function")
-def fxtr_group_roles(fxtr_group):# pylint: disable=[redefined-outer-name]
+def fxtr_group_roles(fxtr_group, fxtr_roles):# pylint: disable=[redefined-outer-name,unused-argument]
"""Link roles to group"""
- from .role_fixtures import RESOURCE_EDITOR_ROLE, RESOURCE_READER_ROLE# pylint: disable=[import-outside-toplevel]
group_roles = (
GroupRole(uuid.UUID("9c25efb2-b477-4918-a95c-9914770cbf4d"),
TEST_GROUP_01, RESOURCE_EDITOR_ROLE),
@@ -96,11 +105,20 @@ def fxtr_group_roles(fxtr_group):# pylint: disable=[redefined-outer-name]
yield conn, groups, group_roles
+ with db.cursor(conn) as cursor:
+ cursor.execute("SELECT * FROM group_user_roles_on_resources")
+ cursor.executemany(
+ ("DELETE FROM group_roles "
+ "WHERE group_role_id=? AND group_id=? AND role_id=?"),
+ ((str(role.group_role_id), str(role.group.group_id),
+ str(role.role.role_id))
+ for role in group_roles))
+
@pytest.fixture(scope="function")
-def fxtr_group_user_roles(fxtr_users_in_group, fxtr_group_roles, fxtr_resources):#pylint: disable=[redefined-outer-name,unused-argument]
+def fxtr_group_user_roles(fxtr_resources, fxtr_group_roles, fxtr_users_in_group):#pylint: disable=[redefined-outer-name,unused-argument]
"""Assign roles to users."""
- from .role_fixtures import RESOURCE_EDITOR_ROLE # pylint: disable=[import-outside-toplevel]
- conn, _groups, _group_roles = fxtr_group_roles
+ conn, _groups, group_roles = fxtr_group_roles
+ _conn, group_resources = fxtr_resources
_conn, _group, group_users = fxtr_users_in_group
users = tuple(user for user in group_users if user.email
not in ("unaff@iliated.user", "group@lead.er"))
@@ -108,19 +126,22 @@ def fxtr_group_user_roles(fxtr_users_in_group, fxtr_group_roles, fxtr_resources)
(user, RESOURCE_EDITOR_ROLE, TEST_RESOURCES_GROUP_01[1])
for user in users if user.email == "group@mem.ber01")
with db.cursor(conn) as cursor:
+ params = tuple({
+ "group_id": str(resource.group.group_id),
+ "user_id": str(user.user_id),
+ "role_id": str(role.role_id),
+ "resource_id": str(resource.resource_id)
+ } for user, role, resource in users_roles_resources)
cursor.executemany(
- ("INSERT INTO group_user_roles_on_resources VALUES (?, ?, ?, ?)"),
- ((str(TEST_GROUP_01.group_id), str(user.user_id), str(role.role_id),
- str(resource.resource_id))
- for user, role, resource in users_roles_resources))
+ ("INSERT INTO group_user_roles_on_resources "
+ "VALUES (:group_id, :user_id, :role_id, :resource_id)"),
+ params)
- yield conn
+ yield conn, group_users, group_roles, group_resources
with db.cursor(conn) as cursor:
cursor.executemany(
("DELETE FROM group_user_roles_on_resources WHERE "
- "group_id=? AND user_id=? AND role_id=? AND "
- "resource_id=?"),
- ((str(TEST_GROUP_01.group_id), str(user.user_id), str(role.role_id),
- str(resource.resource_id))
- for user, role, resource in users_roles_resources))
+ "group_id=:group_id AND user_id=:user_id AND role_id=:role_id AND "
+ "resource_id=:resource_id"),
+ params)
diff --git a/tests/unit/auth/fixtures/resource_fixtures.py b/tests/unit/auth/fixtures/resource_fixtures.py
index 12d8bce..117b4f4 100644
--- a/tests/unit/auth/fixtures/resource_fixtures.py
+++ b/tests/unit/auth/fixtures/resource_fixtures.py
@@ -15,4 +15,11 @@ def fxtr_resources(fxtr_group):# pylint: disable=[redefined-outer-name]
((str(res.group.group_id), str(res.resource_id), res.resource_name,
str(res.resource_category.resource_category_id),
1 if res.public else 0) for res in TEST_RESOURCES))
- return (conn, TEST_RESOURCES)
+
+ yield (conn, TEST_RESOURCES)
+
+ with db.cursor(conn) as cursor:
+ cursor.executemany(
+ "DELETE FROM resources WHERE group_id=? AND resource_id=?",
+ ((str(res.group.group_id), str(res.resource_id),)
+ for res in TEST_RESOURCES))
diff --git a/tests/unit/auth/test_groups.py b/tests/unit/auth/test_groups.py
index 53e0543..158360e 100644
--- a/tests/unit/auth/test_groups.py
+++ b/tests/unit/auth/test_groups.py
@@ -73,10 +73,15 @@ def test_create_group_role(mocker, fxtr_users_in_group, fxtr_app, user, expected
mocker.patch("gn3.auth.authorisation.groups.uuid4", uuid_fn)
mocker.patch("gn3.auth.authorisation.roles.uuid4", uuid_fn)
conn, _group, _users = fxtr_users_in_group
- with fxtr_app.app_context() as flask_context:
+ with fxtr_app.app_context() as flask_context, db.cursor(conn) as cursor:
flask_context.g.user = user
assert create_group_role(
conn, GROUP, "ResourceEditor", PRIVILEGES) == expected
+ # cleanup
+ cursor.execute(
+ ("DELETE FROM group_roles "
+ "WHERE group_role_id=? AND group_id=? AND role_id=?"),
+ (str(uuid_fn()), str(GROUP.group_id), str(uuid_fn())))
@pytest.mark.unit_test
def test_create_multiple_groups(mocker, fxtr_app, fxtr_users):
diff --git a/tests/unit/auth/test_resources.py b/tests/unit/auth/test_resources.py
index b756cd9..e6ebeb9 100644
--- a/tests/unit/auth/test_resources.py
+++ b/tests/unit/auth/test_resources.py
@@ -3,6 +3,7 @@ import uuid
import pytest
+from gn3.auth import db
from gn3.auth.authorisation.groups import Group
from gn3.auth.authorisation.resources import (
Resource, user_resources, create_resource, ResourceCategory,
@@ -35,10 +36,14 @@ def test_create_resource(mocker, fxtr_app, fxtr_users_in_group, user, expected):
"""Test that resource creation works as expected."""
mocker.patch("gn3.auth.authorisation.resources.uuid4", uuid_fn)
conn, _group, _users = fxtr_users_in_group
- with fxtr_app.app_context() as flask_context:
+ with fxtr_app.app_context() as flask_context, db.cursor(conn) as cursor:
flask_context.g.user = user
assert create_resource(conn, "test_resource", resource_category) == expected
+ # Cleanup
+ cursor.execute(
+ "DELETE FROM resources WHERE resource_id=?", (str(uuid_fn()),))
+
SORTKEY = lambda resource: resource.resource_id
@pytest.mark.unit_test
@@ -74,5 +79,5 @@ def test_user_resources(fxtr_group_user_roles, user, expected):
WHEN: a particular user's resources are requested
THEN: list only the resources for which the user can access
"""
- conn = fxtr_group_user_roles
+ conn, *_others = fxtr_group_user_roles
assert sorted(user_resources(conn, user), key=SORTKEY) == expected
diff --git a/tests/unit/auth/test_roles.py b/tests/unit/auth/test_roles.py
index 56ad39e..bee03fc 100644
--- a/tests/unit/auth/test_roles.py
+++ b/tests/unit/auth/test_roles.py
@@ -99,4 +99,5 @@ def test_user_roles(fxtr_group_user_roles, user, expected):
WHEN: we request the user's privileges
THEN: return **ALL** the privileges attached to the user
"""
- assert user_roles(fxtr_group_user_roles, user) == expected
+ conn, *_others = fxtr_group_user_roles
+ assert user_roles(conn, user) == expected
diff --git a/tests/unit/auth/test_token.py b/tests/unit/auth/test_token.py
index a1709bf..76316ea 100644
--- a/tests/unit/auth/test_token.py
+++ b/tests/unit/auth/test_token.py
@@ -2,6 +2,8 @@
import pytest
+from gn3.auth import db
+
SUCCESS_RESULT = {
"status_code": 200,
"result": {
@@ -42,7 +44,7 @@ def test_token(fxtr_app, fxtr_oauth2_clients, test_data, expected):
back
c) TODO: when user tries to use wrong client, we get error message back
"""
- _conn, oa2clients = fxtr_oauth2_clients
+ conn, oa2clients = fxtr_oauth2_clients
email, password, client_idx = test_data
data = {
"grant_type": "password", "scope": "profile nonexistent-scope",
@@ -50,8 +52,11 @@ def test_token(fxtr_app, fxtr_oauth2_clients, test_data, expected):
"client_secret": oa2clients[client_idx].client_secret,
"username": email, "password": password}
- with fxtr_app.test_client() as client:
+ with fxtr_app.test_client() as client, db.cursor(conn) as cursor:
res = client.post("/api/oauth2/token", data=data)
+ # cleanup db
+ cursor.execute("DELETE FROM oauth2_tokens WHERE access_token=?",
+ (gen_token(None, None, None, None),))
assert res.status_code == expected["status_code"]
for key in expected["result"]:
assert res.json[key] == expected["result"][key]
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-18 19:26:32 +0000