From 1a6ed93a8f1def9c9f22df2aa99ea9dbffa2a9ff Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 31 May 2023 17:31:35 +0300 Subject: Use utility.tools to get configuration variables Using flask.current_app.config for configurations does not give the appropriate configurations. --- wqflask/wqflask/oauth2/checks.py | 7 ++++--- wqflask/wqflask/oauth2/client.py | 32 ++++++++++++++++++-------------- wqflask/wqflask/oauth2/data.py | 18 +++++++++++------- wqflask/wqflask/oauth2/request_utils.py | 12 +++++++----- wqflask/wqflask/oauth2/users.py | 14 +++++++------- 5 files changed, 47 insertions(+), 36 deletions(-) diff --git a/wqflask/wqflask/oauth2/checks.py b/wqflask/wqflask/oauth2/checks.py index 3b6d2471..38561c6f 100644 --- a/wqflask/wqflask/oauth2/checks.py +++ b/wqflask/wqflask/oauth2/checks.py @@ -27,11 +27,12 @@ def require_oauth2(func): return redirect("/") def __with_token__(token): + from utility.tools import ( + GN_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET) client = OAuth2Session( - config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"], - token=token) + OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET, token=token) resp = client.get( - urljoin(config["GN_SERVER_URL"], "oauth2/user")) + urljoin(GN_SERVER_URL, "oauth2/user")) user_details = resp.json() if not user_details.get("error", False): return func(*args, **kwargs) diff --git a/wqflask/wqflask/oauth2/client.py b/wqflask/wqflask/oauth2/client.py index b992f0ad..2a06b156 100644 --- a/wqflask/wqflask/oauth2/client.py +++ b/wqflask/wqflask/oauth2/client.py @@ -16,10 +16,11 @@ SCOPE = ("profile group role resource register-client user masquerade " "introspect migrate-data") def oauth2_client(): - config = app.config def __client__(token) -> OAuth2Session: + from utility.tools import ( + GN_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET) return OAuth2Session( - config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"], + OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET, scope=SCOPE, token_endpoint_auth_method="client_secret_post", token=token) return session.user_token().either( @@ -38,12 +39,13 @@ def __no_token__(_err) -> Left: def oauth2_get(uri_path: str, data: dict = {}, **kwargs) -> Either: def __get__(token) -> Either: - config = app.config + from utility.tools import ( + GN_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET) client = OAuth2Session( - config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"], + OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET, token=token, scope=SCOPE) resp = client.get( - urljoin(config["GN_SERVER_URL"], uri_path), + urljoin(GN_SERVER_URL, uri_path), data=data, **kwargs) if resp.status_code == 200: @@ -57,12 +59,13 @@ def oauth2_post( uri_path: str, data: Optional[dict] = None, json: Optional[dict] = None, **kwargs) -> Either: def __post__(token) -> Either: - config = app.config + from utility.tools import ( + GN_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET) client = OAuth2Session( - config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"], + OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET, token=token, scope=SCOPE) resp = client.post( - urljoin(config["GN_SERVER_URL"], uri_path), data=data, json=json, + urljoin(GN_SERVER_URL, uri_path), data=data, json=json, **kwargs) if resp.status_code == 200: return Right(resp.json()) @@ -72,21 +75,22 @@ def oauth2_post( return session.user_token().either(__no_token__, __post__) def no_token_get(uri_path: str, **kwargs) -> Either: - config = app.config - resp = requests.get(urljoin(config["GN_SERVER_URL"], uri_path), **kwargs) + from utility.tools import GN_SERVER_URL + resp = requests.get(urljoin(GN_SERVER_URL, uri_path), **kwargs) if resp.status_code == 200: return Right(resp.json()) return Left(resp) def no_token_post(uri_path: str, **kwargs) -> Either: - config = app.config + from utility.tools import ( + GN_SERVER_URL, OAUTH2_CLIENT_ID, OAUTH2_CLIENT_SECRET) data = kwargs.get("data", {}) the_json = kwargs.get("json", {}) request_data = { **data, **the_json, - "client_id": config["OAUTH2_CLIENT_ID"], - "client_secret": config["OAUTH2_CLIENT_SECRET"] + "client_id": OAUTH2_CLIENT_ID, + "client_secret": OAUTH2_CLIENT_SECRET } new_kwargs = { **{ @@ -95,7 +99,7 @@ def no_token_post(uri_path: str, **kwargs) -> Either: }, ("data" if bool(data) else "json"): request_data } - resp = requests.post(urljoin(config["GN_SERVER_URL"], uri_path), + resp = requests.post(urljoin(GN_SERVER_URL, uri_path), **new_kwargs) if resp.status_code == 200: return Right(resp.json()) diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py index 8b8f4f20..795e9ea3 100644 --- a/wqflask/wqflask/oauth2/data.py +++ b/wqflask/wqflask/oauth2/data.py @@ -18,8 +18,9 @@ from .client import oauth2_get, oauth2_post data = Blueprint("data", __name__) def __search_mrna__(query, template, **kwargs): + from utility.tools import GN_SERVER_URL species_name = kwargs["species_name"] - search_uri = urljoin(app.config["GN_SERVER_URL"], "oauth2/data/search") + search_uri = urljoin(GN_SERVER_URL, "oauth2/data/search") datasets = oauth2_get( "oauth2/data/search", json = { @@ -42,8 +43,9 @@ def __selected_datasets__(): request.form.get("selected", [])) def __search_genotypes__(query, template, **kwargs): + from utility.tools import GN_SERVER_URL species_name = kwargs["species_name"] - search_uri = urljoin(app.config["GN_SERVER_URL"], "oauth2/data/search") + search_uri = urljoin(GN_SERVER_URL, "oauth2/data/search") datasets = oauth2_get( "oauth2/data/search", json = { @@ -57,6 +59,7 @@ def __search_genotypes__(query, template, **kwargs): return render_ui(template, search_uri=search_uri, **datasets, **kwargs) def __search_phenotypes__(query, template, **kwargs): + from utility.tools import GN_SERVER_URL page = int(request.args.get("page", 1)) per_page = int(request.args.get("per_page", 50)) selected_traits = request.form.getlist("selected_traits") @@ -68,10 +71,10 @@ def __search_phenotypes__(query, template, **kwargs): template, traits=[], per_page=per_page, query=query, selected_traits=selected_traits, search_results=search_results, search_endpoint=urljoin( - app.config["GN_SERVER_URL"], "oauth2/data/search"), - gn_server_url = app.config["GN_SERVER_URL"], + GN_SERVER_URL, "oauth2/data/search"), + gn_server_url = GN_SERVER_URL, results_endpoint=urljoin( - app.config["GN_SERVER_URL"], + GN_SERVER_URL, f"oauth2/data/search/phenotype/{job_id}"), **kwargs) return oauth2_get("oauth2/data/search", json={ @@ -79,7 +82,7 @@ def __search_phenotypes__(query, template, **kwargs): "species_name": kwargs["species_name"], "per_page": per_page, "page": page, - "gn3_server_uri": app.config["GN_SERVER_URL"] + "gn3_server_uri": GN_SERVER_URL }).either( lambda err: __search_error__(process_error(err)), __search_success__) @@ -121,6 +124,7 @@ def json_search_mrna() -> Response: @data.route("/phenotype/search", methods=["POST"]) def json_search_phenotypes() -> Response: """Search for phenotypes.""" + from utility.tools import GN_SERVER_URL form = request.json def __handle_error__(err): error = process_error(err) @@ -134,7 +138,7 @@ def json_search_phenotypes() -> Response: "query": form.get("query", ""), "per_page": int(form.get("per_page", 50)), "page": int(form.get("page", 1)), - "gn3_server_uri": app.config["GN_SERVER_URL"], + "gn3_server_uri": GN_SERVER_URL, "selected_traits": form.get("selected_traits", []) }).either(__handle_error__, jsonify) diff --git a/wqflask/wqflask/oauth2/request_utils.py b/wqflask/wqflask/oauth2/request_utils.py index d994cd36..b9f2aa7d 100644 --- a/wqflask/wqflask/oauth2/request_utils.py +++ b/wqflask/wqflask/oauth2/request_utils.py @@ -10,12 +10,13 @@ from flask import ( from .client import SCOPE, oauth2_get def authserver_authorise_uri(): + from utility.tools import GN_SERVER_URL, OAUTH2_CLIENT_ID req_baseurl = urlparse(request.base_url) host_uri = f"{req_baseurl.scheme}://{req_baseurl.netloc}/" return urljoin( - app.config["GN_SERVER_URL"], + GN_SERVER_URL, "oauth2/authorise?response_type=code" - f"&client_id={app.config['OAUTH2_CLIENT_ID']}" + f"&client_id={OAUTH2_CLIENT_ID}" f"&redirect_uri={urljoin(host_uri, 'oauth2/code')}") def raise_unimplemented(): @@ -30,13 +31,14 @@ def process_error(error: Response, message: str=("Requested endpoint was not found on the API " "server.") ) -> dict: - if error.status_code == 404: + if error.status_code in (401, 404): try: - msg = error.json()["error_description"] + err = error.json() + msg = err.get("error_description", f"{error.reason}") except simplejson.errors.JSONDecodeError as _jde: msg = message return { - "error": "NotFoundError", + "error": error.reason, "error_message": msg, "error_description": msg, "status_code": error.status_code diff --git a/wqflask/wqflask/oauth2/users.py b/wqflask/wqflask/oauth2/users.py index 51a4ca4c..1ff23d17 100644 --- a/wqflask/wqflask/oauth2/users.py +++ b/wqflask/wqflask/oauth2/users.py @@ -65,19 +65,19 @@ def request_add_to_group() -> Response: @users.route("/login", methods=["GET", "POST"]) def login(): """Route to allow users to sign up.""" + from utility.tools import GN_SERVER_URL next_endpoint=request.args.get("next", False) if request.method == "POST": form = request.form client = oauth2_client() - config = app.config try: token = client.fetch_token( - urljoin(config["GN_SERVER_URL"], "oauth2/token"), + urljoin(GN_SERVER_URL, "oauth2/token"), username=form.get("email_address"), password=form.get("password"), grant_type="password") - session.set_token(token) + session.set_user_token(token) udets = user_details() session.set_user_details({ "user_id": UUID(udets["user_id"]), @@ -101,10 +101,10 @@ def login(): @users.route("/logout", methods=["GET", "POST"]) def logout(): + from utility.tools import GN_SERVER_URL if user_logged_in(): - config = app.config resp = oauth2_client().revoke_token( - urljoin(config["GN_SERVER_URL"], "oauth2/revoke")) + urljoin(GN_SERVER_URL, "oauth2/revoke")) the_session = session.session_info() if not bool(the_session["masquerading"]): # Normal session - clear and go back. @@ -124,6 +124,7 @@ def logout(): @users.route("/register", methods=["GET", "POST"]) def register_user(): + from utility.tools import GN_SERVER_URL if user_logged_in(): next_endpoint=request.args.get("next", "/") flash(("You cannot register a new user while logged in. " @@ -134,10 +135,9 @@ def register_user(): if request.method == "GET": return render_ui("oauth2/register_user.html") - config = app.config form = request.form response = requests.post( - urljoin(config["GN_SERVER_URL"], "oauth2/user/register"), + urljoin(GN_SERVER_URL, "oauth2/user/register"), data = { "user_name": form.get("user_name"), "email": form.get("email_address"), -- cgit v1.2.3