5 files changed, 42 insertions, 22 deletions
diff --git a/uploader/authorisation.py b/uploader/authorisation.py
index a283980..bc950d8 100644
--- a/uploader/authorisation.py
+++ b/uploader/authorisation.py
@@ -16,13 +16,12 @@ def require_login(function):
     @wraps(function)
     def __is_session_valid__(*args, **kwargs):
         """Check that the user is logged in and their token is valid."""
-        def __clear_session__(_no_token):
-            session.clear_session_info()
-            flash("You need to be signed in.", "alert-danger big-alert")
+        def __alert_needs_sign_in__(_no_token):
+            flash("You need to be signed in.", "alert alert-danger big-alert")
             return redirect("/")
 
         return session.user_token().either(
-            __clear_session__,
+            __alert_needs_sign_in__,
             lambda token: function(*args, **kwargs))
     return __is_session_valid__
 
diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py
index 1efa299..12fbf80 100644
--- a/uploader/oauth2/client.py
+++ b/uploader/oauth2/client.py
@@ -1,6 +1,7 @@
 """OAuth2 client utilities."""
 import json
 import time
+import uuid
 import random
 from datetime import datetime, timedelta
 from urllib.parse import urljoin, urlparse
@@ -146,9 +147,24 @@ def oauth2_client():
         __client__)
 
 
+def fetch_user_details() -> Either:
+    """Retrieve user details from the auth server"""
+    suser = session.session_info()["user"]
+    if suser["email"] == "anon@ymous.user":
+        udets = oauth2_get("auth/user/").then(
+            lambda usrdets: session.set_user_details({
+                "user_id": uuid.UUID(usrdets["user_id"]),
+                "name": usrdets["name"],
+                "email": usrdets["email"],
+                "token": session.user_token()}))
+        return udets
+    return Right(suser)
+
+
 def user_logged_in():
     """Check whether the user has logged in."""
     suser = session.session_info()["user"]
+    fetch_user_details()
     return suser["logged_in"] and suser["token"].is_right()
 
 
diff --git a/uploader/oauth2/views.py b/uploader/oauth2/views.py
index a7211cb..db4ef61 100644
--- a/uploader/oauth2/views.py
+++ b/uploader/oauth2/views.py
@@ -24,22 +24,24 @@ from .client import (
     user_logged_in,
     authserver_uri,
     oauth2_clientid,
+    fetch_user_details,
     oauth2_clientsecret)
 
 oauth2 = Blueprint("oauth2", __name__)
 
+
 @oauth2.route("/code")
 def authorisation_code():
     """Receive authorisation code from auth server and use it to get token."""
     def __process_error__(resp_or_exception):
         app.logger.debug("ERROR: (%s)", resp_or_exception)
         flash("There was an error retrieving the authorisation token.",
-              "alert-danger")
+              "alert alert-danger")
         return redirect("/")
 
     def __fail_set_user_details__(_failure):
         app.logger.debug("Fetching user details fails: %s", _failure)
-        flash("Could not retrieve the user details", "alert-danger")
+        flash("Could not retrieve the user details", "alert alert-danger")
         return redirect("/")
 
     def __success_set_user_details__(_success):
@@ -48,19 +50,13 @@ def authorisation_code():
 
     def __success__(token):
         session.set_user_token(token)
-        return oauth2_get("auth/user/").then(
-            lambda usrdets: session.set_user_details({
-                "user_id": uuid.UUID(usrdets["user_id"]),
-                "name": usrdets["name"],
-                "email": usrdets["email"],
-                "token": session.user_token(),
-                "logged_in": True})).either(
+        return fetch_user_details().either(
                     __fail_set_user_details__,
                     __success_set_user_details__)
 
     code = request.args.get("code", "").strip()
     if not bool(code):
-        flash("AuthorisationError: No code was provided.", "alert-danger")
+        flash("AuthorisationError: No code was provided.", "alert alert-danger")
         return redirect("/")
 
     baseurl = urlparse(request.base_url, scheme=request.scheme)
@@ -116,7 +112,7 @@ def logout():
         _user = session_info["user"]
         _user_str = f"{_user['name']} ({_user['email']})"
         session.clear_session_info()
-        flash("Successfully signed out.", "alert-success")
+        flash("Successfully signed out.", "alert alert-success")
         return redirect("/")
 
     if user_logged_in():
@@ -134,5 +130,5 @@ def logout():
                         cleanup_thunk=lambda: __unset_session__(
                             session.session_info())),
                     lambda res: __unset_session__(session.session_info()))
-    flash("There is no user that is currently logged in.", "alert-info")
+    flash("There is no user that is currently logged in.", "alert alert-info")
     return redirect("/")
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 430a3fb..9c737fc 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -3,6 +3,7 @@ import sys
 import csv
 import uuid
 import json
+import logging
 import datetime
 import tempfile
 from typing import Any
@@ -900,9 +901,9 @@ def edit_download_phenotype_data(# pylint: disable=[unused-argument]
             filename = Path(tmpdir).joinpath("tempfile.tsv")
             with open(filename, mode="w") as outfile:
                 outfile.write(
-                    "# **DO NOT** delete the 'UniqueIdentifier' field. It is used "
-                    "by the system to identify and edit the correct row(s) in the "
-                    "database.\n")
+                    "# **DO NOT** delete the 'UniqueIdentifier' row. It is used "
+                    "by the system to identify and edit the correct rows and "
+                    "columns in the database.\n")
                 outfile.write(
                     "# The '…_description' fields are useful for you to figure out "
                     "what row you are working on. Changing any of this fields will "
@@ -972,8 +973,13 @@ def edit_upload_phenotype_data(# pylint: disable=[unused-argument]
                                        [
                                            sys.executable, "-u",
                                            "-m", "scripts.phenotypes_bulk_edit",
+                                           app.config["SQL_URI"],
                                            jobs_db,
-                                           str(job_id)
+                                           str(job_id),
+                                           "--log-level",
+                                           logging.getLevelName(
+                                               app.logger.getEffectiveLevel()
+                                           ).lower()
                                        ],
                                        "phenotype-bulk-edit",
                                        extra_meta = {
diff --git a/uploader/session.py b/uploader/session.py
index b538187..5af5827 100644
--- a/uploader/session.py
+++ b/uploader/session.py
@@ -77,12 +77,15 @@ def set_user_token(token: str) -> SessionInfo:
     """Set the user's token."""
     info = session_info()
     return save_session_info({
-        **info, "user": {**info["user"], "token": Right(token)}})#type: ignore[misc]
+        **info,
+        "user": {**info["user"], "token": Right(token), "logged_in": True}
+    })#type: ignore[misc]
 
 
 def set_user_details(userdets: UserDetails) -> SessionInfo:
     """Set the user details information"""
-    return save_session_info({**session_info(), "user": userdets})#type: ignore[misc]
+    info = session_info()
+    return save_session_info({**info, "user": {**info["user"], **userdets}})#type: ignore[misc]
 
 def user_details() -> UserDetails:
     """Retrieve user details."""