diff options
Diffstat (limited to 'gn_auth/auth/authorisation/data')
| -rw-r--r-- | gn_auth/auth/authorisation/data/genotypes.py | 2 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/mrna.py | 2 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/phenotypes.py | 36 | ||||
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 30 |
4 files changed, 50 insertions, 20 deletions
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py index 7cae91a..ddb0add 100644 --- a/gn_auth/auth/authorisation/data/genotypes.py +++ b/gn_auth/auth/authorisation/data/genotypes.py @@ -22,7 +22,7 @@ def linked_genotype_data(conn: authdb.DbConnection) -> Iterable[dict]: "You do not have sufficient privileges to link data to (a) " "group(s)."), oauth2_scope="profile group resource") -def ungrouped_genotype_data(# pylint: disable=[too-many-arguments] +def ungrouped_genotype_data(# pylint: disable=[too-many-arguments, too-many-positional-arguments] authconn: authdb.DbConnection, gn3conn: gn3db.Connection, search_query: str, selected: tuple[dict, ...] = tuple(), limit: int = 10000, offset: int = 0) -> tuple[ diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py index 82a0f82..0cc644e 100644 --- a/gn_auth/auth/authorisation/data/mrna.py +++ b/gn_auth/auth/authorisation/data/mrna.py @@ -22,7 +22,7 @@ def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]: "You do not have sufficient privileges to link data to (a) " "group(s)."), oauth2_scope="profile group resource") -def ungrouped_mrna_data(# pylint: disable=[too-many-arguments] +def ungrouped_mrna_data(# pylint: disable=[too-many-arguments, too-many-positional-arguments] authconn: authdb.DbConnection, gn3conn: gn3db.Connection, search_query: str, selected: tuple[dict, ...] = tuple(), limit: int = 10000, offset: int = 0) -> tuple[ diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py index 08a0524..3e45af3 100644 --- a/gn_auth/auth/authorisation/data/phenotypes.py +++ b/gn_auth/auth/authorisation/data/phenotypes.py @@ -8,8 +8,12 @@ from MySQLdb.cursors import DictCursor from gn_auth.auth.db import sqlite3 as authdb +from gn_auth.auth.errors import AuthorisationError from gn_auth.auth.authorisation.checks import authorised_p -from gn_auth.auth.authorisation.resources.groups.models import Group +from gn_auth.auth.authorisation.resources.system.models import system_resource +from gn_auth.auth.authorisation.resources.groups.models import Group, group_resource + +from gn_auth.auth.authorisation.resources.checks import authorised_for2 def linked_phenotype_data( authconn: authdb.DbConnection, gn3conn: gn3db.Connection, @@ -83,7 +87,7 @@ def ungrouped_phenotype_data( return tuple() -def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]: +def pheno_traits_from_db(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dict, ...]: """An internal utility function. Don't use outside of this module.""" if len(params) < 1: return tuple() @@ -110,21 +114,33 @@ def __traits__(gn3conn: gn3db.Connection, params: tuple[dict, ...]) -> tuple[dic for itm in sublist)) return cursor.fetchall() -@authorised_p(("system:data:link-to-group",), - error_description=( - "You do not have sufficient privileges to link data to (a) " - "group(s)."), - oauth2_scope="profile group resource") + def link_phenotype_data( - authconn:authdb.DbConnection, gn3conn: gn3db.Connection, group: Group, - traits: tuple[dict, ...]) -> dict: + authconn: authdb.DbConnection, + user, + group: Group, + traits: tuple[dict, ...] +) -> dict: """Link phenotype traits to a user group.""" + if not (authorised_for2(authconn, + user, + system_resource(authconn), + ("system:data:link-to-group",)) + or + authorised_for2(authconn, + user, + group_resource(authconn, group.group_id), + ("group:data:link-to-group",)) + ): + raise AuthorisationError( + "You do not have sufficient privileges to link data to group " + f"'{group.group_name}'.") with authdb.cursor(authconn) as cursor: params = tuple({ "data_link_id": str(uuid.uuid4()), "group_id": str(group.group_id), **item - } for item in __traits__(gn3conn, traits)) + } for item in traits) cursor.executemany( "INSERT INTO linked_phenotype_data " "VALUES (" diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 38eaad6..9123949 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -35,8 +35,8 @@ from ..resources.models import ( from ...authentication.users import User from ...authentication.oauth2.resource_server import require_oauth -from ..data.phenotypes import link_phenotype_data 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 data = Blueprint("data", __name__) @@ -189,7 +189,7 @@ def __search_mrna__(): def __request_key__(key: str, default: Any = ""): if bool(request_json()): return request_json().get(#type: ignore[union-attr] - key, request.args.get(key, request_json().get(key, default))) + key, request.args.get(key, default)) return request.args.get(key, request_json().get(key, default)) def __request_key_list__(key: str, default: tuple[Any, ...] = tuple()): @@ -312,6 +312,7 @@ def link_mrna() -> Response: partial(__link__, **__values__(request_json())))) @data.route("/link/phenotype", methods=["POST"]) +@require_oauth("profile group resource") def link_phenotype() -> Response: """Link phenotype data to group.""" def __values__(form): @@ -327,14 +328,27 @@ def link_phenotype() -> Response: raise InvalidData("Expected at least one dataset to be provided.") return { "group_id": uuid.UUID(form["group_id"]), - "traits": form["selected"] + "traits": form["selected"], + "using_raw_ids": bool(form.get("using-raw-ids") == "on") } - with gn3db.database_connection(app.config["SQL_URI"]) as gn3conn: - def __link__(conn: db.DbConnection, group_id: uuid.UUID, - traits: tuple[dict, ...]) -> dict: - return link_phenotype_data( - conn, gn3conn, group_by_id(conn, group_id), traits) + with (require_oauth.acquire("profile group resource") as token, + gn3db.database_connection(app.config["SQL_URI"]) as gn3conn): + def __link__( + conn: db.DbConnection, + group_id: uuid.UUID, + traits: tuple[dict, ...], + using_raw_ids: bool = False + ) -> dict: + if using_raw_ids: + return link_phenotype_data(conn, + token.user, + group_by_id(conn, group_id), + traits) + return link_phenotype_data(conn, + token.user, + group_by_id(conn, group_id), + pheno_traits_from_db(gn3conn, traits)) return jsonify(with_db_connection( partial(__link__, **__values__(request_json())))) |