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-rw-r--r--gn_auth/auth/authorisation/data/genotypes.py6
-rw-r--r--gn_auth/auth/authorisation/data/mrna.py7
-rw-r--r--gn_auth/auth/authorisation/data/phenotypes.py42
-rw-r--r--gn_auth/auth/authorisation/data/views.py34
4 files changed, 61 insertions, 28 deletions
diff --git a/gn_auth/auth/authorisation/data/genotypes.py b/gn_auth/auth/authorisation/data/genotypes.py
index bdab8fa..ddb0add 100644
--- a/gn_auth/auth/authorisation/data/genotypes.py
+++ b/gn_auth/auth/authorisation/data/genotypes.py
@@ -3,9 +3,9 @@ import uuid
from dataclasses import asdict
from typing import Iterable
+from gn_libs import mysqldb as gn3db
from MySQLdb.cursors import DictCursor
-from gn_auth.auth.db import mariadb as gn3db
from gn_auth.auth.db import sqlite3 as authdb
from gn_auth.auth.authorisation.checks import authorised_p
@@ -22,8 +22,8 @@ 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]
- authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
+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[
dict, ...]:
diff --git a/gn_auth/auth/authorisation/data/mrna.py b/gn_auth/auth/authorisation/data/mrna.py
index 60470a7..0cc644e 100644
--- a/gn_auth/auth/authorisation/data/mrna.py
+++ b/gn_auth/auth/authorisation/data/mrna.py
@@ -2,10 +2,11 @@
import uuid
from dataclasses import asdict
from typing import Iterable
+
+from gn_libs import mysqldb as gn3db
from MySQLdb.cursors import DictCursor
from gn_auth.auth.db import sqlite3 as authdb
-from gn_auth.auth.db import mariadb as gn3db
from gn_auth.auth.authorisation.checks import authorised_p
from gn_auth.auth.authorisation.resources.groups.models import Group
@@ -21,8 +22,8 @@ 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]
- authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
+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[
dict, ...]:
diff --git a/gn_auth/auth/authorisation/data/phenotypes.py b/gn_auth/auth/authorisation/data/phenotypes.py
index 0a76237..3e45af3 100644
--- a/gn_auth/auth/authorisation/data/phenotypes.py
+++ b/gn_auth/auth/authorisation/data/phenotypes.py
@@ -3,16 +3,20 @@ import uuid
from dataclasses import asdict
from typing import Any, Iterable
+from gn_libs import mysqldb as gn3db
from MySQLdb.cursors import DictCursor
from gn_auth.auth.db import sqlite3 as authdb
-from gn_auth.auth.db import mariadb as gn3db
+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.DbConnection,
+ authconn: authdb.DbConnection, gn3conn: gn3db.Connection,
species: str = "") -> Iterable[dict[str, Any]]:
"""Retrieve phenotype data linked to user groups."""
authkeys = ("SpeciesId", "InbredSetId", "PublishFreezeId", "PublishXRefId")
@@ -53,7 +57,7 @@ def linked_phenotype_data(
"group(s)."),
oauth2_scope="profile group resource")
def ungrouped_phenotype_data(
- authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection):
+ authconn: authdb.DbConnection, gn3conn: gn3db.Connection):
"""Retrieve phenotype data that is not linked to any user group."""
with gn3conn.cursor() as cursor:
params = tuple(
@@ -83,7 +87,7 @@ def ungrouped_phenotype_data(
return tuple()
-def __traits__(gn3conn: gn3db.DbConnection, 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.DbConnection, params: tuple[dict, ...]) -> tuple[d
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.DbConnection, 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 7ed69e3..9123949 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -11,6 +11,9 @@ from MySQLdb.cursors import DictCursor
from authlib.integrations.flask_oauth2.errors import _HTTPException
from flask import request, jsonify, Response, Blueprint, current_app as app
+
+from gn_libs import mysqldb as gn3db
+
from gn_auth import jobs
from gn_auth.commands import run_async_cmd
@@ -19,7 +22,6 @@ from gn_auth.auth.errors import InvalidData, NotFoundError
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
from ..checks import require_json
@@ -33,8 +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__)
@@ -187,7 +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()):
@@ -310,6 +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):
@@ -325,14 +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()))))
generated by cgit v1.2.3 (git 2.47.1) at 2025-07-01 18:35:57 +0000