diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 78 |
1 files changed, 65 insertions, 13 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index c90b072..49c12b5 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -4,14 +4,17 @@ import csv import uuid import json import logging -import datetime import tempfile from typing import Any from pathlib import Path from zipfile import ZipFile +from urllib.parse import urljoin from functools import wraps, reduce from logging import INFO, ERROR, DEBUG, FATAL, CRITICAL, WARNING +import datetime +from datetime import timedelta + from redis import Redis from pymonad.either import Left from requests.models import Response @@ -21,7 +24,9 @@ from werkzeug.utils import secure_filename from gn_libs import sqlite3 from gn_libs import jobs as gnlibs_jobs from gn_libs.mysqldb import database_connection +from gn_libs import monadic_requests as mrequests +from authlib.jose import jwt from flask import (flash, request, url_for, @@ -35,11 +40,14 @@ from flask import (flash, from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe + from uploader import jobs +from uploader import session from uploader.files import save_file#, fullpath from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login +from uploader.oauth2 import jwks, client as oauth2client from uploader.route_utils import generic_select_population from uploader.datautils import safe_int, enumerate_sequence from uploader.species.models import all_species, species_by_id @@ -640,21 +648,65 @@ def load_data_to_database( app.logger.getEffectiveLevel() ).lower() ] - load_job = gnlibs_jobs.launch_job( - gnlibs_jobs.initialise_job(conn, - load_job_id, - command, - "load-new-phenotypes-data", - extra_meta={ - "species_id": species["SpeciesId"], - "population_id": population["Id"], - "dataset_id": dataset["Id"], - "bundle_file": _meta["bundle"] - }), + + def __handle_error__(resp): + raise Exception(resp) + + def __handle_success__(load_job): + app.logger.debug("The phenotypes loading job: %s", load_job) + return str(load_job) + issued = datetime.datetime.now() + jwtkey = jwks.newest_jwk_with_rotation( + jwks.jwks_directory(app, "UPLOADER_SECRETS"), + int(app.config["JWKS_ROTATION_AGE_DAYS"])) + + return mrequests.post( + urljoin(oauth2client.authserver_uri(), "auth/token"), + json={ + "grant_type": "urn:ietf:params:oauth:grant-type:jwt-bearer", + "scope": oauth2client.SCOPE, + "assertion": jwt.encode( + header={ + "alg": "RS256", + "typ": "JWT", + "kid": jwtkey.as_dict()["kid"] + }, + payload={ + "iss": str(oauth2client.oauth2_clientid()), + "sub": str(session.user_details()["user_id"]), + "aud": urljoin(oauth2client.authserver_uri(), + "auth/token"), + # TODO: Update expiry time once fix is implemented in + # auth server. + "exp": (issued + timedelta(minutes=5)).timestamp(), + "nbf": int(issued.timestamp()), + "iat": int(issued.timestamp()), + "jti": str(uuid.uuid4()) + }, + key=jwtkey).decode("utf8"), + "client_id": oauth2client.oauth2_clientid() + } + ).then( + lambda token: gnlibs_jobs.initialise_job( + conn, + load_job_id, + command, + "load-new-phenotypes-data", + extra_meta={ + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": dataset["Id"], + "bundle_file": _meta["bundle"], + "authserver": oauth2client.authserver_uri(), + "token": token["access_token"] + }) + ).then( + lambda job: gnlibs_jobs.launch_job( + job, jobs_db, f"{app.config['UPLOAD_FOLDER']}/job_errors", worker_manager="gn_libs.jobs.launcher") - return str(load_job) + ).either(__handle_error__, __handle_success__) def update_phenotype_metadata(conn, metadata: dict): |