diff options
Diffstat (limited to 'gn_auth/auth/authorisation/data/views.py')
| -rw-r--r-- | gn_auth/auth/authorisation/data/views.py | 62 |
1 files changed, 40 insertions, 22 deletions
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py index 83f4e4b..4bf6746 100644 --- a/gn_auth/auth/authorisation/data/views.py +++ b/gn_auth/auth/authorisation/data/views.py @@ -11,14 +11,17 @@ 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 +from gn_auth.auth.requests import request_json 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 @@ -32,11 +35,12 @@ 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.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): """ @@ -184,18 +188,18 @@ def __search_mrna__(): return jsonify(with_db_connection(__ungrouped__)) 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.form.get(key, default))) - return request.args.get(key, request.form.get(key, default)) + if bool(request_json()): + return request_json().get(#type: ignore[union-attr] + 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()): - if bool(request.json): - return (request.json.get(key,[])#type: ignore[union-attr] - or request.args.getlist(key) or request.form.getlist(key) + if bool(request_json()): + return (request_json().get(key,[])#type: ignore[union-attr] + or request.args.getlist(key) or request_json().get(key) or list(default)) return (request.args.getlist(key) - or request.form.getlist(key) or list(default)) + or request_json().get(key) or list(default)) def __search_genotypes__(): query = __request_key__("query", "") @@ -240,7 +244,7 @@ def __search_phenotypes__(): @require_oauth("profile group resource") def search_unlinked_data(): """Search for various unlinked data.""" - dataset_type = request.json["dataset_type"] + dataset_type = request_json()["dataset_type"] search_fns = { "mrna": __search_mrna__, "genotype": __search_genotypes__, @@ -281,7 +285,7 @@ def link_genotypes() -> Response: return link_genotype_data(conn, group_by_id(conn, group_id), datasets) return jsonify(with_db_connection( - partial(__link__, **__values__(request.json)))) + partial(__link__, **__values__(request_json())))) @data.route("/link/mrna", methods=["POST"]) def link_mrna() -> Response: @@ -306,9 +310,10 @@ def link_mrna() -> Response: return link_mrna_data(conn, group_by_id(conn, group_id), datasets) return jsonify(with_db_connection( - partial(__link__, **__values__(request.json)))) + 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): @@ -324,14 +329,27 @@ 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)))) + partial(__link__, **__values__(request_json())))) |