Use utility.tools to get configuration variables

Using flask.current_app.config for configurations does not give the
appropriate configurations.

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"),