Move `groups` package under `resources` package

With user groups being resources that users can act on (with the
recent changes), this commit moves the `groups` module to under the
`resources` module.

It also renames the `*_resources.py` modules by dropping the
`_resources` part since the code is under the `resources` module
anyway.

16 files changed, 119 insertions, 107 deletions

diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index 818f72d..bfddfc1 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -4,12 +4,12 @@ from typing import Iterable
 
 from MySQLdb.cursors import DictCursor
 
-from ..checks import authorised_p
-from ..groups.models import Group
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db import sqlite3 as authdb
 
-from ...dictify import dictify
-from ...db import mariadb as gn3db
-from ...db import sqlite3 as authdb
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.resources.groups.models import Group
 
 def linked_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]:
     """Retrive genotype data that is linked to user groups."""
diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
index 53f9bf9..edcd29e 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -3,12 +3,12 @@ import uuid
 from typing import Iterable
 from MySQLdb.cursors import DictCursor
 
-from ..checks import authorised_p
-from ..groups.models import Group
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.db import sqlite3 as authdb
+from gn_auth.auth.db import mariadb as gn3db
 
-from ...dictify import dictify
-from ...db import sqlite3 as authdb
-from ...db import mariadb as gn3db
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.resources.groups.models import Group
 
 def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
     """Retrieve mRNA Assay data that is linked to user groups."""
diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py
index 84fc089..17555ec 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -4,13 +4,12 @@ from typing import Any, Iterable
 
 from MySQLdb.cursors import DictCursor
 
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.db import sqlite3 as authdb
+from gn_auth.auth.db import mariadb as gn3db
 
-from ..checks import authorised_p
-from ..groups.models import Group
-
-from ...dictify import dictify
-from ...db import sqlite3 as authdb
-from ...db import mariadb as gn3db
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.resources.groups.models import Group
 
 def linked_phenotype_data(
         authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index 3c49ae5..a674ab4 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -13,6 +13,8 @@ from flask import request, jsonify, Response, Blueprint, current_app as app
 from gn_auth import jobs
 from gn_auth.commands import run_async_cmd
 
+from gn_auth.auth.authorisation.resources.groups.models import group_by_id
+
 from ...db import sqlite3 as db
 from ...db import mariadb as gn3db
 from ...db.sqlite3 import with_db_connection
@@ -20,8 +22,6 @@ from ...db.sqlite3 import with_db_connection
 from ..checks import require_json
 from ..errors import InvalidData, NotFoundError
 
-from ..groups.models import group_by_id
-
 from ..users.models import user_resource_roles
 
 from ..resources.checks import authorised_for
diff --git a/gn_auth/auth/authorisation/resources/errors.py b/gn_auth/auth/authorisation/resources/errors.py
new file mode 100644
index 0000000..dc6c379
--- /dev/null
+++ b/gn_auth/auth/authorisation/resources/errors.py
@@ -0,0 +1,6 @@
+"""Exceptions for Authorisation"""
+
+from gn_auth.auth.authorisation.errors import AuthorisationError
+
+class MissingGroupError(AuthorisationError):
+    """Raised for any resource operation without a group."""
diff --git a/gn_auth/auth/authorisation/resources/genotype_resource.py b/gn_auth/auth/authorisation/resources/genotype.py
index 206ab61..206ab61 100644
--- a/gn_auth/auth/authorisation/resources/genotype_resource.py
+++ b/gn_auth/auth/authorisation/resources/genotype.py
diff --git a/gn_auth/auth/authorisation/groups/__init__.py b/gn_auth/auth/authorisation/resources/groups/__init__.py
index 1cb0bba..1cb0bba 100644
--- a/gn_auth/auth/authorisation/groups/__init__.py
+++ b/gn_auth/auth/authorisation/resources/groups/__init__.py
diff --git a/gn_auth/auth/authorisation/groups/data.py b/gn_auth/auth/authorisation/resources/groups/data.py
index 1650405..9fcdc6e 100644
--- a/gn_auth/auth/authorisation/groups/data.py
+++ b/gn_auth/auth/authorisation/resources/groups/data.py
@@ -1,12 +1,12 @@
 """Handles the resource objects' data."""
 from MySQLdb.cursors import DictCursor
 
-from ..groups import Group
-from ..checks import authorised_p
-from ..errors import NotFoundError
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db import sqlite3 as authdb
 
-from ...db import mariadb as gn3db
-from ...db import sqlite3 as authdb
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.errors import NotFoundError
+from gn_auth.auth.authorisation.resources.groups import Group
 
 def __fetch_mrna_data_by_ids__(
         conn: gn3db.DbConnection, dataset_ids: tuple[str, ...]) -> tuple[
diff --git a/gn_auth/auth/authorisation/groups/models.py b/gn_auth/auth/authorisation/resources/groups/models.py
index c40adbd..5ec26c5 100644
--- a/gn_auth/auth/authorisation/groups/models.py
+++ b/gn_auth/auth/authorisation/resources/groups/models.py
@@ -7,14 +7,17 @@ from typing import Any, Sequence, Iterable, Optional, NamedTuple
 from flask import g
 from pymonad.maybe import Just, Maybe, Nothing
 
-from ...db import sqlite3 as db
-from ...dictify import dictify
-from ...authentication.users import User, user_by_id
-
-from ..checks import authorised_p
-from ..privileges import Privilege
-from ..errors import NotFoundError, AuthorisationError, InconsistencyError
-from ..roles.models import (
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.authentication.users import User, user_by_id
+
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.privileges import Privilege
+from gn_auth.auth.authorisation.resources.base import Resource
+from gn_auth.auth.authorisation.resources.errors import MissingGroupError
+from gn_auth.auth.authorisation.errors import (
+    NotFoundError, AuthorisationError, InconsistencyError)
+from gn_auth.auth.authorisation.roles.models import (
     Role, create_role, check_user_editable, revoke_user_role_by_name,
     assign_user_role_by_name)
 
@@ -431,3 +434,20 @@ def delete_privilege_from_group_role(
                  group_role.role.user_editable,
                  tuple(priv for priv in group_role.role.privileges
                        if priv != privilege)))
+
+def resource_owner(conn: db.DbConnection, resource: Resource) -> Group:
+    """Return the user group that owns the resource."""
+    with db.cursor(conn) as cursor:
+        cursor.execute(
+            "SELECT g.* FROM resource_ownership AS ro "
+            "INNER JOIN groups AS g ON ro.group_id=g.group_id "
+            "WHERE ro.resource_id=?",
+            (str(resource.resource_id),))
+        row = cursor.fetchone()
+        if row:
+            return Group(
+                UUID(row["group_id"]),
+                row["group_name"],
+                json.loads(row["group_metadata"]))
+
+    raise MissingGroupError("Resource has no 'owning' group.")
diff --git a/gn_auth/auth/authorisation/groups/views.py b/gn_auth/auth/authorisation/resources/groups/views.py
index 4dc17e0..f146ffd 100644
--- a/gn_auth/auth/authorisation/groups/views.py
+++ b/gn_auth/auth/authorisation/resources/groups/views.py
@@ -1,4 +1,6 @@
-"""The views/routes for the `gn3.auth.authorisation.groups` package."""
+"""
+The views/routes for the `gn3.auth.authorisation.resources.groups` package.
+"""
 import uuid
 import datetime
 from typing import Iterable
@@ -7,11 +9,20 @@ from functools import partial
 from MySQLdb.cursors import DictCursor
 from flask import request, jsonify, Response, Blueprint, current_app
 
-from ...db import sqlite3 as db
-from ...db import mariadb as gn3db
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.db import mariadb as gn3db
+from gn_auth.auth.db.sqlite3 import with_db_connection
+from gn_auth.auth.dictify import dictify
 
-from ...dictify import dictify
-from ...db.sqlite3 import with_db_connection
+from gn_auth.auth.authorisation.roles.models import Role
+from gn_auth.auth.authorisation.roles.models import user_roles
+
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.privileges import Privilege, privileges_by_ids
+from gn_auth.auth.authorisation.errors import InvalidData, NotFoundError, AuthorisationError
+
+from gn_auth.auth.authentication.users import User
+from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
 
 from .data import link_data_to_group
 from .models import (
@@ -21,16 +32,6 @@ from .models import (
     create_group as _create_group, add_privilege_to_group_role,
     delete_privilege_from_group_role, create_group_role as _create_group_role)
 
-from ..roles.models import Role
-from ..roles.models import user_roles
-
-from ..checks import authorised_p
-from ..privileges import Privilege, privileges_by_ids
-from ..errors import InvalidData, NotFoundError, AuthorisationError
-
-from ...authentication.users import User
-from ...authentication.oauth2.resource_server import require_oauth
-
 groups = Blueprint("groups", __name__)
 
 @groups.route("/list", methods=["GET"])
diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py
index f307fdc..80820a5 100644
--- a/gn_auth/auth/authorisation/resources/models.py
+++ b/gn_auth/auth/authorisation/resources/models.py
@@ -1,38 +1,37 @@
 """Handle the management of resources."""
-import json
 from uuid import UUID, uuid4
 from functools import reduce, partial
 from typing import Dict, Sequence, Optional
 
-from ...db import sqlite3 as db
-from ...dictify import dictify
-from ...authentication.users import User
-from ...db.sqlite3 import with_db_connection
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.authentication.users import User
+from gn_auth.auth.db.sqlite3 import with_db_connection
 
-from ..checks import authorised_p
-from ..errors import NotFoundError, AuthorisationError
-from ..groups.models import Group, GroupRole, user_group, is_group_leader
+from gn_auth.auth.authorisation.checks import authorised_p
+from gn_auth.auth.authorisation.errors import NotFoundError, AuthorisationError
 
 from .checks import authorised_for
 from .base import Resource, ResourceCategory
-from .mrna_resource import (
+from .groups.models import (
+    Group, GroupRole, user_group, resource_owner, is_group_leader)
+from .mrna import (
     resource_data as mrna_resource_data,
     attach_resources_data as mrna_attach_resources_data,
     link_data_to_resource as mrna_link_data_to_resource,
     unlink_data_from_resource as mrna_unlink_data_from_resource)
-from .genotype_resource import (
+from .genotype import (
     resource_data as genotype_resource_data,
     attach_resources_data as genotype_attach_resources_data,
     link_data_to_resource as genotype_link_data_to_resource,
     unlink_data_from_resource as genotype_unlink_data_from_resource)
-from .phenotype_resource import (
+from .phenotype import (
     resource_data as phenotype_resource_data,
     attach_resources_data as phenotype_attach_resources_data,
     link_data_to_resource as phenotype_link_data_to_resource,
     unlink_data_from_resource as phenotype_unlink_data_from_resource)
 
-class MissingGroupError(AuthorisationError):
-    """Raised for any resource operation without a group."""
+from .errors import MissingGroupError
 
 def __assign_resource_owner_role__(cursor, resource, user, group):
     """Assign `user` the 'Resource Owner' role for `resource`."""
@@ -73,7 +72,7 @@ def create_resource(
         group = user_group(conn, user).maybe(
             False, lambda grp: grp)# type: ignore[misc, arg-type]
         if not group:
-            raise MissingGroupError(
+            raise MissingGroupError(# Not all resources require an owner group
                 "User with no group cannot create a resource.")
         resource = Resource(uuid4(), resource_name, resource_category, public)
         cursor.execute(
@@ -246,7 +245,7 @@ def link_data_to_resource(
         "genotype": genotype_link_data_to_resource,
         "phenotype": phenotype_link_data_to_resource,
     }[dataset_type.lower()](
-        conn, resource, resource_group(conn, resource), data_link_id)
+        conn, resource, resource_owner(conn, resource), data_link_id)
 
 def unlink_data_from_resource(
         conn: db.DbConnection, user: User, resource_id: UUID, data_link_id: UUID):
@@ -367,20 +366,3 @@ def save_resource(
 
     raise AuthorisationError(
         "You do not have the appropriate privileges to edit this resource.")
-
-def resource_group(conn: db.DbConnection, resource: Resource) -> Group:
-    """Return the group that owns the resource."""
-    with db.cursor(conn) as cursor:
-        cursor.execute(
-            "SELECT g.* FROM resource_ownership AS ro "
-            "INNER JOIN groups AS g ON ro.group_id=g.group_id "
-            "WHERE ro.resource_id=?",
-            (str(resource.resource_id),))
-        row = cursor.fetchone()
-        if row:
-            return Group(
-                UUID(row["group_id"]),
-                row["group_name"],
-                json.loads(row["group_metadata"]))
-
-    raise MissingGroupError("Resource has no 'owning' group.")
diff --git a/gn_auth/auth/authorisation/resources/mrna_resource.py b/gn_auth/auth/authorisation/resources/mrna.py
index 7fce227..7fce227 100644
--- a/gn_auth/auth/authorisation/resources/mrna_resource.py
+++ b/gn_auth/auth/authorisation/resources/mrna.py
diff --git a/gn_auth/auth/authorisation/resources/phenotype_resource.py b/gn_auth/auth/authorisation/resources/phenotype.py
index 046357c..cd3f23d 100644
--- a/gn_auth/auth/authorisation/resources/phenotype_resource.py
+++ b/gn_auth/auth/authorisation/resources/phenotype.py
@@ -5,8 +5,8 @@ from typing import Optional, Sequence
 import sqlite3
 
 import gn_auth.auth.db.sqlite3 as db
-from gn_auth.auth.authorisation.groups import Group
 
+from .groups import Group
 from .base import Resource
 from .data import __attach_data__
 
diff --git a/gn_auth/auth/authorisation/resources/views.py b/gn_auth/auth/authorisation/resources/views.py
index 4fe04d9..0e44df5 100644
--- a/gn_auth/auth/authorisation/resources/views.py
+++ b/gn_auth/auth/authorisation/resources/views.py
@@ -6,23 +6,23 @@ from functools import reduce
 
 from flask import request, jsonify, Response, Blueprint, current_app as app
 
-from ...db import sqlite3 as db
-from ...db.sqlite3 import with_db_connection
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.db.sqlite3 import with_db_connection
+
+from gn_auth.auth.authorisation.roles import Role
+from gn_auth.auth.authorisation.errors import InvalidData, InconsistencyError, AuthorisationError
+
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
+from gn_auth.auth.authentication.users import User, user_by_id, user_by_email
 
 from .checks import authorised_for
 from .models import (
-    Resource, save_resource, resource_data, resource_group, resource_by_id,
+    Resource, save_resource, resource_data, resource_by_id,
     resource_categories, assign_resource_user, link_data_to_resource,
     unassign_resource_user, resource_category_by_id, unlink_data_from_resource,
     create_resource as _create_resource)
-
-from ..roles import Role
-from ..errors import InvalidData, InconsistencyError, AuthorisationError
-from ..groups.models import Group, GroupRole, group_role_by_id
-
-from ...dictify import dictify
-from ...authentication.oauth2.resource_server import require_oauth
-from ...authentication.users import User, user_by_id, user_by_email
+from .groups.models import Group, GroupRole, resource_owner, group_role_by_id
 
 resources = Blueprint("resources", __name__)
 
@@ -165,7 +165,7 @@ def resource_users(resource_id: uuid.UUID):
                             "user", User(user_id, row["email"], row["name"]))
                         role = GroupRole(
                             uuid.UUID(row["group_role_id"]),
-                            resource_group(conn, resource),
+                            resource_owner(conn, resource),
                             Role(uuid.UUID(row["role_id"]), row["role_name"],
                                  bool(int(row["user_editable"])), tuple()))
                         return {
@@ -222,7 +222,7 @@ def assign_role_to_user(resource_id: uuid.UUID) -> Response:
                 return assign_resource_user(
                     conn, resource, user,
                     group_role_by_id(conn,
-                                     resource_group(conn, resource),
+                                     resource_owner(conn, resource),
                                      uuid.UUID(group_role_id)))
         except AssertionError as aserr:
             raise AuthorisationError(aserr.args[0]) from aserr
@@ -246,7 +246,7 @@ def unassign_role_to_user(resource_id: uuid.UUID) -> Response:
                 return unassign_resource_user(
                     conn, resource, user_by_id(conn, uuid.UUID(user_id)),
                     group_role_by_id(conn,
-                                     resource_group(conn, resource),
+                                     resource_owner(conn, resource),
                                      uuid.UUID(group_role_id)))
         except AssertionError as aserr:
             raise AuthorisationError(aserr.args[0]) from aserr
diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py
index 6de30da..50386ac 100644
--- a/gn_auth/auth/authorisation/users/views.py
+++ b/gn_auth/auth/authorisation/users/views.py
@@ -7,24 +7,28 @@ import sqlite3
 from email_validator import validate_email, EmailNotValidError
 from flask import request, jsonify, Response, Blueprint, current_app
 
-from ...db import sqlite3 as db
-from ...dictify import dictify
-from ...db.sqlite3 import with_db_connection
+from gn_auth.auth.db import sqlite3 as db
+from gn_auth.auth.dictify import dictify
+from gn_auth.auth.db.sqlite3 import with_db_connection
+
+from gn_auth.auth.authorisation.resources.models import (
+    user_resources as _user_resources)
+from gn_auth.auth.authorisation.roles.models import (
+    assign_default_roles, user_roles as _user_roles)
+from gn_auth.auth.authorisation.errors import (
+    NotFoundError, UsernameError, PasswordError, UserRegistrationError)
+from gn_auth.auth.authorisation.resources.groups.models import (
+    user_group as _user_group)
+
+from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
+from gn_auth.auth.authentication.users import User, save_user, set_user_password
+from gn_auth.auth.authentication.oauth2.models.oauth2token import (
+    token_by_access_token)
 
 from .models import list_users
 from .masquerade.views import masq
 from .collections.views import collections
 
-from ..groups.models import user_group as _user_group
-from ..resources.models import user_resources as _user_resources
-from ..roles.models import assign_default_roles, user_roles as _user_roles
-from ..errors import (
-    NotFoundError, UsernameError, PasswordError, UserRegistrationError)
-
-from ...authentication.oauth2.resource_server import require_oauth
-from ...authentication.users import User, save_user, set_user_password
-from ...authentication.oauth2.models.oauth2token import token_by_access_token
-
 users = Blueprint("users", __name__)
 users.register_blueprint(masq, url_prefix="/masquerade")
 users.register_blueprint(collections, url_prefix="/collections")
diff --git a/gn_auth/auth/views.py b/gn_auth/auth/views.py
index 56eace7..cd1cb6f 100644
--- a/gn_auth/auth/views.py
+++ b/gn_auth/auth/views.py
@@ -7,8 +7,8 @@ from .authorisation.data.views import data
 from .authorisation.users.views import users
 from .authorisation.users.admin import admin
 from .authorisation.roles.views import roles
-from .authorisation.groups.views import groups
 from .authorisation.resources.views import resources
+from .authorisation.resources.groups.views import groups
 
 oauth2 = Blueprint("oauth2", __name__)