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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-pink 1.4.1 (git 2.36.1) at 2025-10-05 22:55:28 +0000