Copy over files from GN3 repository.

7 files changed, 393 insertions, 0 deletions

diff --git a/tests/unit/auth/fixtures/__init__.py b/tests/unit/auth/fixtures/__init__.py
new file mode 100644
index 0000000..a675fc7
--- /dev/null
+++ b/tests/unit/auth/fixtures/__init__.py
@@ -0,0 +1,8 @@
+"""pytest's conftest as a module."""
+from .role_fixtures import *
+from .user_fixtures import *
+from .group_fixtures import *
+from .resource_fixtures import *
+# from .privilege_fixtures import *
+from .migration_fixtures import *
+from .oauth2_client_fixtures import *
diff --git a/tests/unit/auth/fixtures/group_fixtures.py b/tests/unit/auth/fixtures/group_fixtures.py
new file mode 100644
index 0000000..d7bbc56
--- /dev/null
+++ b/tests/unit/auth/fixtures/group_fixtures.py
@@ -0,0 +1,147 @@
+"""Fixtures and utilities for group-related tests"""
+import uuid
+
+import pytest
+
+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"),
+                      "AnotherTestGroup", {})
+TEST_GROUPS = (TEST_GROUP_01, TEST_GROUP_02)
+
+TEST_RESOURCES_GROUP_01 = (
+    Resource(TEST_GROUPS[0], uuid.UUID("26ad1668-29f5-439d-b905-84d551f85955"),
+             "ResourceG01R01",
+             ResourceCategory(uuid.UUID("48056f84-a2a6-41ac-8319-0e1e212cba2a"),
+                              "genotype", "Genotype Dataset"),
+             True),
+    Resource(TEST_GROUPS[0], uuid.UUID("2130aec0-fefd-434d-92fd-9ca342348b2d"),
+             "ResourceG01R02",
+             ResourceCategory(uuid.UUID("548d684b-d4d1-46fb-a6d3-51a56b7da1b3"),
+                              "phenotype", "Phenotype (Publish) Dataset"),
+             False),
+    Resource(TEST_GROUPS[0], uuid.UUID("e9a1184a-e8b4-49fb-b713-8d9cbeea5b83"),
+             "ResourceG01R03",
+             ResourceCategory(uuid.UUID("fad071a3-2fc8-40b8-992b-cdefe7dcac79"),
+                              "mrna", "mRNA Dataset"),
+             False))
+
+TEST_RESOURCES_GROUP_02 = (
+    Resource(TEST_GROUPS[1], uuid.UUID("14496a1c-c234-49a2-978c-8859ea274054"),
+             "ResourceG02R01",
+             ResourceCategory(uuid.UUID("48056f84-a2a6-41ac-8319-0e1e212cba2a"),
+                              "genotype", "Genotype Dataset"),
+             False),
+    Resource(TEST_GROUPS[1], uuid.UUID("04ad9e09-94ea-4390-8a02-11f92999806b"),
+             "ResourceG02R02",
+             ResourceCategory(uuid.UUID("fad071a3-2fc8-40b8-992b-cdefe7dcac79"),
+                              "mrna", "mRNA Dataset"),
+             True))
+
+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."""
+    query = "INSERT INTO groups(group_id, group_name) VALUES (?, ?)"
+    with db.cursor(conn_after_auth_migrations) as cursor:
+        cursor.executemany(
+            query, tuple(
+                (str(group.group_id), group.group_name)
+                for group in TEST_GROUPS))
+
+    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."""
+    conn, all_users = fxtr_users
+    users = tuple(
+        user for user in all_users if user.email not in ("unaff@iliated.user",))
+    query_params = tuple(
+        (str(TEST_GROUP_01.group_id), str(user.user_id)) for user in users)
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "INSERT INTO group_users(group_id, user_id) VALUES (?, ?)",
+            query_params)
+
+    yield (conn, TEST_GROUP_01, users)
+
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "DELETE FROM group_users WHERE group_id=? AND user_id=?",
+            query_params)
+
+@pytest.fixture(scope="function")
+def fxtr_group_roles(fxtr_group, fxtr_roles):# pylint: disable=[redefined-outer-name,unused-argument]
+    """Link roles to group"""
+    group_roles = (
+        GroupRole(uuid.UUID("9c25efb2-b477-4918-a95c-9914770cbf4d"),
+                  TEST_GROUP_01, RESOURCE_EDITOR_ROLE),
+        GroupRole(uuid.UUID("82aed039-fe2f-408c-ab1e-81cd1ba96630"),
+                  TEST_GROUP_02, RESOURCE_READER_ROLE))
+    conn, groups = fxtr_group
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "INSERT INTO group_roles VALUES (?, ?, ?)",
+            ((str(role.group_role_id), str(role.group.group_id),
+              str(role.role.role_id))
+             for role in group_roles))
+
+    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_resources, fxtr_group_roles, fxtr_users_in_group):#pylint: disable=[redefined-outer-name,unused-argument]
+    """Assign roles to users."""
+    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"))
+    users_roles_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 (:group_id, :user_id, :role_id, :resource_id)"),
+            params)
+
+    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=: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/migration_fixtures.py b/tests/unit/auth/fixtures/migration_fixtures.py
new file mode 100644
index 0000000..eb42c2b
--- /dev/null
+++ b/tests/unit/auth/fixtures/migration_fixtures.py
@@ -0,0 +1,51 @@
+"""Fixtures and utilities for migration-related tests"""
+import pytest
+from yoyo.backends import DatabaseBackend
+from yoyo import get_backend, read_migrations
+from yoyo.migrations import Migration, MigrationList
+
+from gn3.auth import db
+from gn3.migrations import apply_migrations, rollback_migrations
+
+@pytest.fixture(scope="session")
+def auth_testdb_path(fxtr_app_config): # pylint: disable=redefined-outer-name
+    """Get the test application's auth database file"""
+    return fxtr_app_config["AUTH_DB"]
+
+@pytest.fixture(scope="session")
+def auth_migrations_dir(fxtr_app_config): # pylint: disable=redefined-outer-name
+    """Get the test application's auth database file"""
+    return fxtr_app_config["AUTH_MIGRATIONS"]
+
+def apply_single_migration(backend: DatabaseBackend, migration: Migration):# pylint: disable=[redefined-outer-name]
+    """Utility to apply a single migration"""
+    apply_migrations(backend, MigrationList([migration]))
+
+def rollback_single_migration(backend: DatabaseBackend, migration: Migration):# pylint: disable=[redefined-outer-name]
+    """Utility to rollback a single migration"""
+    rollback_migrations(backend, MigrationList([migration]))
+
+@pytest.fixture(scope="session")
+def backend(auth_testdb_path):# pylint: disable=redefined-outer-name
+    """Fixture: retrieve yoyo backend for auth database"""
+    return get_backend(f"sqlite:///{auth_testdb_path}")
+
+@pytest.fixture(scope="session")
+def all_migrations(auth_migrations_dir): # pylint: disable=redefined-outer-name
+    """Retrieve all the migrations"""
+    return read_migrations(auth_migrations_dir)
+
+@pytest.fixture(scope="function")
+def conn_after_auth_migrations(backend, auth_testdb_path, all_migrations): # pylint: disable=redefined-outer-name
+    """Run all migrations and return a connection to the database after"""
+    apply_migrations(backend, all_migrations)
+    with db.connection(auth_testdb_path) as conn:
+        yield conn
+
+    rollback_migrations(backend, all_migrations)
+
+def migrations_up_to(migration, migrations_dir):
+    """Run all the migration before `migration`."""
+    migrations = read_migrations(migrations_dir)
+    index = [mig.path for mig in migrations].index(migration)
+    return MigrationList(migrations[0:index])
diff --git a/tests/unit/auth/fixtures/oauth2_client_fixtures.py b/tests/unit/auth/fixtures/oauth2_client_fixtures.py
new file mode 100644
index 0000000..654d048
--- /dev/null
+++ b/tests/unit/auth/fixtures/oauth2_client_fixtures.py
@@ -0,0 +1,51 @@
+"""Fixtures for OAuth2 clients"""
+import uuid
+import json
+import datetime
+
+import pytest
+
+from gn3.auth import db
+from gn3.auth.authentication.users import hash_password
+from gn3.auth.authentication.oauth2.models.oauth2client import OAuth2Client
+
+@pytest.fixture(autouse=True)
+def fxtr_patch_envvars(monkeypatch):
+    """Fixture: patch environment variable"""
+    monkeypatch.setenv("AUTHLIB_INSECURE_TRANSPORT", "true")
+
+@pytest.fixture
+def fxtr_oauth2_clients(fxtr_users_with_passwords):
+    """Fixture: Create the OAuth2 clients for use with tests."""
+    conn, users = fxtr_users_with_passwords
+    now = datetime.datetime.now()
+
+    clients = tuple(
+        OAuth2Client(str(uuid.uuid4()), f"yabadabadoo_{idx:03}", now,
+         now + datetime.timedelta(hours = 2),
+         {
+             "client_name": f"test_client_{idx:03}",
+             "scope": ["profile", "group", "role", "resource", "register-client"],
+             "redirect_uri": "/test_oauth2",
+             "token_endpoint_auth_method": [
+                 "client_secret_post", "client_secret_basic"],
+             "grant_types": ["password", "authorisation_code", "refresh_token"],
+            "response_type": "token"
+         }, user)
+        for idx, user  in enumerate(users, start=1))
+
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "INSERT INTO oauth2_clients VALUES (?, ?, ?, ?, ?, ?)",
+            ((str(client.client_id), hash_password(client.client_secret),
+              int(client.client_id_issued_at.timestamp()),
+              int(client.client_secret_expires_at.timestamp()),
+              json.dumps(client.client_metadata), str(client.user.user_id))
+            for client in clients))
+
+    yield conn, clients
+
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "DELETE FROM oauth2_clients WHERE client_id=?",
+            ((str(client.client_id),) for client in clients))
diff --git a/tests/unit/auth/fixtures/resource_fixtures.py b/tests/unit/auth/fixtures/resource_fixtures.py
new file mode 100644
index 0000000..117b4f4
--- /dev/null
+++ b/tests/unit/auth/fixtures/resource_fixtures.py
@@ -0,0 +1,25 @@
+"""Fixtures and utilities for resource-related tests"""
+import pytest
+
+from gn3.auth import db
+
+from .group_fixtures import TEST_RESOURCES
+
+@pytest.fixture(scope="function")
+def fxtr_resources(fxtr_group):# pylint: disable=[redefined-outer-name]
+    """fixture: setup test resources in the database"""
+    conn, _group = fxtr_group
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "INSERT INTO resources VALUES (?,?,?,?,?)",
+        ((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))
+
+    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/fixtures/role_fixtures.py b/tests/unit/auth/fixtures/role_fixtures.py
new file mode 100644
index 0000000..ee86aa2
--- /dev/null
+++ b/tests/unit/auth/fixtures/role_fixtures.py
@@ -0,0 +1,45 @@
+"""Fixtures and utilities for role-related tests"""
+import uuid
+
+import pytest
+
+from gn3.auth import db
+from gn3.auth.authorisation.roles import Role
+from gn3.auth.authorisation.privileges import Privilege
+
+RESOURCE_READER_ROLE = Role(
+    uuid.UUID("c3ca2507-ee24-4835-9b31-8c21e1c072d3"), "resource_reader", True,
+    (Privilege("group:resource:view-resource",
+               "view a resource and use it in computations"),))
+
+RESOURCE_EDITOR_ROLE = Role(
+    uuid.UUID("89819f84-6346-488b-8955-86062e9eedb7"), "resource_editor", True,
+    (
+        Privilege("group:resource:view-resource",
+                  "view a resource and use it in computations"),
+        Privilege("group:resource:edit-resource", "edit/update a resource")))
+
+TEST_ROLES = (RESOURCE_READER_ROLE, RESOURCE_EDITOR_ROLE)
+
+@pytest.fixture(scope="function")
+def fxtr_roles(conn_after_auth_migrations):
+    """Setup some example roles."""
+    with db.cursor(conn_after_auth_migrations) as cursor:
+        cursor.executemany(
+            ("INSERT INTO roles VALUES (?, ?, ?)"),
+            ((str(role.role_id), role.role_name, 1) for role in TEST_ROLES))
+        cursor.executemany(
+            ("INSERT INTO role_privileges VALUES (?, ?)"),
+            ((str(role.role_id), str(privilege.privilege_id))
+             for role in TEST_ROLES for privilege in role.privileges))
+
+    yield conn_after_auth_migrations, TEST_ROLES
+
+    with db.cursor(conn_after_auth_migrations) as cursor:
+        cursor.executemany(
+            ("DELETE FROM role_privileges WHERE role_id=? AND privilege_id=?"),
+            ((str(role.role_id), str(privilege.privilege_id))
+             for role in TEST_ROLES for privilege in role.privileges))
+        cursor.executemany(
+            ("DELETE FROM roles WHERE role_id=?"),
+            ((str(role.role_id),) for role in TEST_ROLES))
diff --git a/tests/unit/auth/fixtures/user_fixtures.py b/tests/unit/auth/fixtures/user_fixtures.py
new file mode 100644
index 0000000..d248f54
--- /dev/null
+++ b/tests/unit/auth/fixtures/user_fixtures.py
@@ -0,0 +1,66 @@
+"""Fixtures and utilities for user-related tests"""
+import uuid
+
+import pytest
+
+from gn3.auth import db
+from gn3.auth.authentication.users import User, hash_password
+
+TEST_USERS = (
+        User(uuid.UUID("ecb52977-3004-469e-9428-2a1856725c7f"), "group@lead.er",
+             "Group Leader"),
+        User(uuid.UUID("21351b66-8aad-475b-84ac-53ce528451e3"),
+             "group@mem.ber01", "Group Member 01"),
+        User(uuid.UUID("ae9c6245-0966-41a5-9a5e-20885a96bea7"),
+             "group@mem.ber02", "Group Member 02"),
+        User(uuid.UUID("9a0c7ce5-2f40-4e78-979e-bf3527a59579"),
+             "unaff@iliated.user", "Unaffiliated User"))
+
+@pytest.fixture(scope="function")
+def fxtr_users(conn_after_auth_migrations):# pylint: disable=[redefined-outer-name]
+    """Fixture: setup test users."""
+    query = "INSERT INTO users(user_id, email, name) VALUES (?, ?, ?)"
+    query_user_roles = "INSERT INTO user_roles(user_id, role_id) VALUES (?, ?)"
+    test_user_roles = (
+        ("ecb52977-3004-469e-9428-2a1856725c7f",
+         "a0e67630-d502-4b9f-b23f-6805d0f30e30"),
+        ("ecb52977-3004-469e-9428-2a1856725c7f",
+         "ade7e6b0-ba9c-4b51-87d0-2af7fe39a347"))
+    with db.cursor(conn_after_auth_migrations) as cursor:
+        cursor.executemany(query, (
+            (str(user.user_id), user.email, user.name) for user in TEST_USERS))
+        cursor.executemany(query_user_roles, test_user_roles)
+
+    yield (conn_after_auth_migrations, TEST_USERS)
+
+    with db.cursor(conn_after_auth_migrations) as cursor:
+        cursor.executemany(
+            "DELETE FROM user_roles WHERE user_id=?",
+            (("ecb52977-3004-469e-9428-2a1856725c7f",),))
+        cursor.executemany(
+            "DELETE FROM users WHERE user_id=?",
+            (("ecb52977-3004-469e-9428-2a1856725c7f",),
+             ("21351b66-8aad-475b-84ac-53ce528451e3",),
+             ("ae9c6245-0966-41a5-9a5e-20885a96bea7",),
+             ("9a0c7ce5-2f40-4e78-979e-bf3527a59579",)))
+
+@pytest.fixture(scope="function")
+def fxtr_users_with_passwords(fxtr_users): # pylint: disable=[redefined-outer-name]
+    """Fixture: add passwords to the users"""
+    conn, users = fxtr_users
+    user_passwords_params = tuple(
+        (str(user.user_id), hash_password(
+            f"password_for_user_{idx:03}".encode("utf8")))
+        for idx, user in enumerate(users, start=1))
+
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "INSERT INTO user_credentials VALUES (?, ?)",
+            user_passwords_params)
+
+    yield conn, users
+
+    with db.cursor(conn) as cursor:
+        cursor.executemany(
+            "DELETE FROM user_credentials WHERE user_id=?",
+            ((item[0],) for item in user_passwords_params))