diff options
| -rw-r--r-- | .guix-channel | 4 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/phenotypes.py | 134 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 7 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/checks.py | 5 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/models.py | 15 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/resources/system/models.py | 17 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/collections/models.py | 4 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/users/views.py | 4 | ||||
| -rw-r--r-- | migrations/auth/20260206_01_v3f4P-add-role-systemwide-data-curator.py | 61 | ||||
| -rwxr-xr-x | setup.py | 2 |
10 files changed, 234 insertions, 19 deletions
diff --git a/.guix-channel b/.guix-channel index 2c37401..bfc31db 100644 --- a/.guix-channel +++ b/.guix-channel @@ -34,11 +34,12 @@ (channel (name guix-bioinformatics) (url "https://git.genenetwork.org/guix-bioinformatics") - (commit "903465c85c9b2ae28480b236c3364da873ca8f51")) + (commit "9b0955f14ec725990abb1f6af3b9f171e4943f77")) (channel (name guix-past) (url "https://codeberg.org/guix-science/guix-past") (branch "master") + (commit "473c942b509ab3ead35159d27dfbf2031a36cd4d") (introduction (channel-introduction (version 0) @@ -49,6 +50,7 @@ (name guix-rust-past-crates) (url "https://codeberg.org/guix/guix-rust-past-crates.git") (branch "trunk") + (commit "b8b7ffbd1cec9f56f93fae4da3a74163bbc9c570") (introduction (channel-introduction (version 0) diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py index 3e45af3..1f79e0e 100644 --- a/gn_auth/auth/authorisation/data/phenotypes.py +++ b/gn_auth/auth/authorisation/data/phenotypes.py @@ -4,17 +4,24 @@ from dataclasses import asdict from typing import Any, Iterable from gn_libs import mysqldb as gn3db +from gn_libs import sqlite3 as authdb from MySQLdb.cursors import DictCursor +from flask import request, jsonify, Response, Blueprint, current_app as app -from gn_auth.auth.db import sqlite3 as authdb +from gn_auth.auth.authentication.oauth2.resource_server import require_oauth from gn_auth.auth.errors import AuthorisationError from gn_auth.auth.authorisation.checks import authorised_p from gn_auth.auth.authorisation.resources.system.models import system_resource +from gn_auth.auth.authorisation.resources.checks import authorised_for_spec from gn_auth.auth.authorisation.resources.groups.models import Group, group_resource + +from gn_auth.auth.authorisation.checks import require_json from gn_auth.auth.authorisation.resources.checks import authorised_for2 +phenosbp = Blueprint("phenotypes", __name__) + def linked_phenotype_data( authconn: authdb.DbConnection, gn3conn: gn3db.Connection, species: str = "") -> Iterable[dict[str, Any]]: @@ -155,3 +162,128 @@ def link_phenotype_data( "group": asdict(group), "traits": params } + + +def unlink_from_resources( + cursor: authdb.DbCursor, + data_link_ids: tuple[uuid.UUID, ...] +) -> tuple[uuid.UUID, ...]: + """Unlink phenotypes from resources.""" + # TODO: Delete in batches + cursor.executemany("DELETE FROM phenotype_resources " + "WHERE data_link_id=? RETURNING resource_id", + tuple((str(_id),) for _id in data_link_ids)) + return tuple(uuid.UUID(row["resource_id"]) for row in cursor.fetchall()) + + +def delete_resources( + cursor: authdb.DbCursor, + resource_ids: tuple[uuid.UUID, ...] +) -> tuple[uuid.UUID, ...]: + """Delete the specified phenotype resources.""" + # TODO: Delete in batches + cursor.executemany("DELETE FROM resources " + "WHERE resource_id=? RETURNING resource_id", + tuple((str(_id),) for _id in resource_ids)) + return tuple(uuid.UUID(row["resource_id"]) for row in cursor.fetchall()) + + +def fetch_data_link_ids( + cursor: authdb.DbCursor, + species_id: int, + population_id: int, + dataset_id: int, + xref_ids: tuple[int, ...] +) -> tuple[uuid.UUID, ...]: + """Fetch `data_link_id` values for phenotypes.""" + paramstr = ", ".join(["(?, ?, ?, ?)"] * len(xref_ids)) + cursor.execute( + "SELECT data_link_id FROM linked_phenotype_data " + "WHERE (SpeciesId, InbredSetId, PublishFreezeId, PublishXRefId) IN " + f"({paramstr})", + tuple(str(field) for arow in + ((species_id, population_id, dataset_id, xref_id) + for xref_id in xref_ids) + for field in arow)) + return tuple(uuid.UUID(row["data_link_id"]) for row in cursor.fetchall()) + + +def fetch_resource_id(cursor: authdb.DbCursor, + data_link_ids: tuple[uuid.UUID, ...]) -> uuid.UUID: + """Retrieve the ID of the resource where the data is linked to. + + RAISES: InvalidResourceError in the case where more the data_link_ids belong + to more than one resource.""" + _paramstr = ", ".join(["?"] * len(data_link_ids)) + cursor.execute( + "SELECT DISTINCT(resource_id) FROM phenotype_resources " + f"WHERE data_link_id IN ({_paramstr})", + tuple(str(_id) for _id in data_link_ids)) + _ids = tuple(uuid.UUID(row['resource_id']) for row in cursor.fetchall()) + if len(_ids) != 1: + raise AuthorisationError( + f"Expected data from 1 resource, got {len(_ids)} resources.") + return _ids[0] + + +def delete_linked_data( + cursor: authdb.DbCursor, + data_link_ids: tuple[uuid.UUID, ...] +) -> int: + """Delete the actual linked data.""" + # TODO: Delete in batches + cursor.executemany("DELETE FROM linked_phenotype_data " + "WHERE data_link_id=?", + tuple((str(_id),) for _id in data_link_ids)) + return cursor.rowcount + + +@phenosbp.route("/<int:species_id>/<int:population_id>/<int:dataset_id>/delete", + methods=["POST"]) +@require_json +def delete_linked_phenotypes_data( + species_id: int, + population_id: int, + dataset_id: int +) -> Response: + """Delete the linked phenotypes data from the database.""" + db_uri = app.config["AUTH_DB"] + with (require_oauth.acquire("profile group resource") as _token, + authdb.connection(db_uri) as auth_conn, + authdb.cursor(auth_conn) as cursor): + # - Does user have DELETE privilege on system (i.e. is data curator)? + # YES: go ahead and delete data as below. + # - Does user have DELETE privilege on resource(s)? + # YES: Delete phenotypes by resource, checking privileges for each + # resource. + # - Neither: Raise `AuthorisationError` and bail! + _deleted = 0 + xref_ids = tuple(request.json.get("xref_ids", []))#type: ignore[union-attr] + if len(xref_ids) > 0: + # TODO: Use background job, for huge number of xref_ids + data_link_ids = fetch_data_link_ids( + cursor, species_id, population_id, dataset_id, xref_ids) + resource_id = fetch_resource_id(cursor, data_link_ids) + if not (authorised_for_spec( + auth_conn, + _token.user.user_id, + resource_id, + "(OR group:resource:delete-resource system:resource:delete)") + or + authorised_for_spec( + auth_conn, + _token.user.user_id, + system_resource(auth_conn).resource_id, + "(AND system:system-wide:data:delete)")): + raise AuthorisationError( + "You are not allowed to delete this resource's data.") + _resources_ids = unlink_from_resources(cursor, data_link_ids) + delete_resources(cursor, _resources_ids) + _deleted = delete_linked_data(cursor, data_link_ids) + + return jsonify({ + # TODO: "status": "sent-to-background"/"completed"/"failed" + # TODO: "status-url": <status-check-uri> + "requested": len(xref_ids), + "deleted": _deleted + }) diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 9123949..4bf6746 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -35,11 +35,12 @@ from ..resources.models import ( from ...authentication.users import User from ...authentication.oauth2.resource_server import require_oauth -from ..data.mrna import link_mrna_data, ungrouped_mrna_data -from ..data.phenotypes import link_phenotype_data, pheno_traits_from_db -from ..data.genotypes import link_genotype_data, ungrouped_genotype_data +from .mrna import link_mrna_data, ungrouped_mrna_data +from .genotypes import link_genotype_data, ungrouped_genotype_data +from .phenotypes import phenosbp, link_phenotype_data, pheno_traits_from_db data = Blueprint("data", __name__) +data.register_blueprint(phenosbp, url_prefix="/phenotypes") def build_trait_name(trait_fullname): """ diff --git a/gn_auth/auth/authorisation/resources/checks.py b/gn_auth/auth/authorisation/resources/checks.py index ce2b821..59bf90c 100644 --- a/gn_auth/auth/authorisation/resources/checks.py +++ b/gn_auth/auth/authorisation/resources/checks.py @@ -1,5 +1,6 @@ """Handle authorisation checks for resources""" import uuid +import logging import warnings from functools import reduce from typing import Sequence @@ -13,6 +14,10 @@ from ...authentication.users import User from ..privileges.models import db_row_to_privilege + +logger = logging.getLogger(__name__) + + def __organise_privileges_by_resource_id__(rows): def __organise__(privs, row): resource_id = uuid.UUID(row["resource_id"]) diff --git a/gn_auth/auth/authorisation/resources/models.py b/gn_auth/auth/authorisation/resources/models.py index 31371fd..a4df363 100644 --- a/gn_auth/auth/authorisation/resources/models.py +++ b/gn_auth/auth/authorisation/resources/models.py @@ -2,9 +2,10 @@ from dataclasses import asdict from uuid import UUID, uuid4 from functools import reduce, partial -from typing import Dict, Sequence, Optional +from typing import Dict, Union, Sequence, Optional + +from gn_libs import sqlite3 as db -from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.authentication.users import User from gn_auth.auth.db.sqlite3 import with_db_connection @@ -40,7 +41,7 @@ from .phenotypes.models import ( error_description="Insufficient privileges to create a resource", oauth2_scope="profile resource") def create_resource(# pylint: disable=[too-many-arguments, too-many-positional-arguments] - conn: db.DbConnection, + conn: Union[db.DbConnection, db.DbCursor], resource_name: str, resource_category: ResourceCategory, user: User, @@ -48,7 +49,7 @@ def create_resource(# pylint: disable=[too-many-arguments, too-many-positional-a public: bool ) -> Resource: """Create a resource item.""" - with db.cursor(conn) as cursor: + def __create_resource__(cursor: db.DbCursor) -> Resource: resource = Resource(uuid4(), resource_name, resource_category, public) cursor.execute( "INSERT INTO resources VALUES (?, ?, ?, ?)", @@ -75,6 +76,12 @@ def create_resource(# pylint: disable=[too-many-arguments, too-many-positional-a return resource + if hasattr(conn, "cursor"): # This is a connection: get its cursor. + with db.cursor(conn) as cursor: + return __create_resource__(cursor) + else: + return __create_resource__(conn) + def delete_resource(conn: db.DbConnection, resource_id: UUID): """Delete a resource.""" diff --git a/gn_auth/auth/authorisation/resources/system/models.py b/gn_auth/auth/authorisation/resources/system/models.py index 303b0ac..25089fa 100644 --- a/gn_auth/auth/authorisation/resources/system/models.py +++ b/gn_auth/auth/authorisation/resources/system/models.py @@ -1,9 +1,10 @@ """Base functions and utilities for system resources.""" from uuid import UUID from functools import reduce -from typing import Sequence +from typing import Union, Sequence + +from gn_libs import sqlite3 as db -from gn_auth.auth.db import sqlite3 as db from gn_auth.auth.errors import NotFoundError from gn_auth.auth.authentication.users import User @@ -52,9 +53,9 @@ def user_roles_on_system(conn: db.DbConnection, user: User) -> Sequence[Role]: return tuple() -def system_resource(conn: db.DbConnection) -> Resource: +def system_resource(conn: Union[db.DbConnection, db.DbCursor]) -> Resource: """Retrieve the system resource.""" - with db.cursor(conn) as cursor: + def __fetch_sys_resource__(cursor: db.DbCursor) -> Resource: cursor.execute( "SELECT resource_categories.*, resources.resource_id, " "resources.resource_name, resources.public " @@ -65,4 +66,10 @@ def system_resource(conn: db.DbConnection) -> Resource: if row: return resource_from_dbrow(row) - raise NotFoundError("Could not find a system resource!") + raise NotFoundError("Could not find a system resource!") + + if hasattr(conn, "cursor"): # is connection + with db.cursor(conn) as cursor: + return __fetch_sys_resource__(cursor) + else: + return __fetch_sys_resource__(conn) diff --git a/gn_auth/auth/authorisation/users/collections/models.py b/gn_auth/auth/authorisation/users/collections/models.py index 63443ef..30242c2 100644 --- a/gn_auth/auth/authorisation/users/collections/models.py +++ b/gn_auth/auth/authorisation/users/collections/models.py @@ -72,8 +72,8 @@ def __retrieve_old_accounts__(rconn: Redis) -> dict: def parse_collection(coll: dict) -> dict: """Parse the collection as persisted in redis to a usable python object.""" - created = coll.get("created", coll.get("created_timestamp")) - changed = coll.get("changed", coll.get("changed_timestamp")) + created = coll.get("created", coll.get("created_timestamp", "")) + changed = coll.get("changed", coll.get("changed_timestamp", "")) return { "id": UUID(coll["id"]), "name": coll["name"], diff --git a/gn_auth/auth/authorisation/users/views.py b/gn_auth/auth/authorisation/users/views.py index cae2605..c248ac3 100644 --- a/gn_auth/auth/authorisation/users/views.py +++ b/gn_auth/auth/authorisation/users/views.py @@ -4,9 +4,9 @@ import sqlite3 import secrets import traceback from dataclasses import asdict -from typing import Any, Sequence from urllib.parse import urljoin from functools import reduce, partial +from typing import Any, Union, Sequence from datetime import datetime, timedelta from email.headerregistry import Address from email_validator import validate_email, EmailNotValidError @@ -80,7 +80,7 @@ def user_details() -> Response: }) @users.route("/<user_id>", methods=["GET"]) -def get_user(user_id: str) -> Response: +def get_user(user_id: str) -> Union[Response, tuple[Response, int]]: """Fetch user details by user_id.""" try: with db.connection(current_app.config["AUTH_DB"]) as conn: diff --git a/migrations/auth/20260206_01_v3f4P-add-role-systemwide-data-curator.py b/migrations/auth/20260206_01_v3f4P-add-role-systemwide-data-curator.py new file mode 100644 index 0000000..63e807a --- /dev/null +++ b/migrations/auth/20260206_01_v3f4P-add-role-systemwide-data-curator.py @@ -0,0 +1,61 @@ +""" +add role systemwide-data-curator. +""" +import uuid +import contextlib + +from yoyo import step + +__depends__ = {'20250731_01_Ke1us-add-sysadmin-privileges-for-acting-on-groups-members'} + + +def create_systemwide_data_curator_role(conn): + """Create a new 'systemwide-data-curator' role.""" + with contextlib.closing(conn.cursor()) as cursor: + cursor.execute( + "INSERT INTO roles(role_id, role_name, user_editable) " + "VALUES (?, 'systemwide-data-curator', 0)", + (str(uuid.uuid4()),)) + + +def link_privileges_to_role(conn): + with contextlib.closing(conn.cursor()) as cursor: + cursor.execute("SELECT role_id FROM roles " + "WHERE role_name='systemwide-data-curator'") + role_id = cursor.fetchone()[0] + cursor.executemany("INSERT INTO role_privileges(role_id, privilege_id) " + "VALUES (?, ?)", + tuple((role_id, priv) for priv in + ("system:system-wide:data:edit", + "system:system-wide:data:delete"))) + + +def unlink_privileges_from_role(conn): + with contextlib.closing(conn.cursor()) as cursor: + cursor.execute("SELECT role_id FROM roles " + "WHERE role_name='systemwide-data-curator'") + role_id = cursor.fetchone()[0] + cursor.executemany("DELETE FROM role_privileges " + "WHERE role_id=? AND privilege_id=?", + tuple((role_id, priv) for priv in + ("system:system-wide:data:edit", + "system:system-wide:data:delete"))) + + +steps = [ + step(# Add new privileges + """ + INSERT INTO privileges (privilege_id, privilege_description) + VALUES + ('system:system-wide:data:edit', + 'A user with this privilege can edit any data on the entire system.'), + ('system:system-wide:data:delete', + 'A user with this privilege can delete any data from the system.') + """, + """ + DELETE FROM privileges WHERE privilege_id IN + ('system:system-wide:data:edit', 'system:system-wide:data:delete')"""), + step(create_systemwide_data_curator_role, + "DELETE FROM roles WHERE role_name='systemwide-data-curator'"), + step(link_privileges_to_role, unlink_privileges_from_role) +] diff --git a/setup.py b/setup.py index 59cd86f..c7339e2 100755 --- a/setup.py +++ b/setup.py @@ -44,5 +44,5 @@ setup(author="Frederick M. Muriithi", version="0.0.1", tests_require=["pytest", "hypothesis"], cmdclass={ - "run_tests": RunTests # testing + "run_tests": RunTests # type: ignore[dict-item] }) |