From 477c3f34f8af919592c722cc1a71b2602cb7ac82 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 12 Jul 2023 14:32:23 +0300
Subject: Use new session to get user (author) information

* wqflask/utility/json/__init__.py: Custom JSON for serialising UUIDs
  into a JSON representantion
* wqflask/utility/json/encoders.py: Custom JSON for serialising UUIDs
  into a JSON representation
* wqflask/wqflask/metadata_edits.py: Use new sessions for author
  information
---
 wqflask/utility/json/__init__.py  |  3 +++
 wqflask/utility/json/encoders.py  | 17 +++++++++++++++++
 wqflask/wqflask/metadata_edits.py | 13 +++++++------
 3 files changed, 27 insertions(+), 6 deletions(-)
 create mode 100644 wqflask/utility/json/__init__.py
 create mode 100644 wqflask/utility/json/encoders.py

(limited to 'wqflask')

diff --git a/wqflask/utility/json/__init__.py b/wqflask/utility/json/__init__.py
new file mode 100644
index 00000000..b1141a34
--- /dev/null
+++ b/wqflask/utility/json/__init__.py
@@ -0,0 +1,3 @@
+"""Local JSON utilities."""
+
+from .encoders import CustomJSONEncoder
diff --git a/wqflask/utility/json/encoders.py b/wqflask/utility/json/encoders.py
new file mode 100644
index 00000000..7c5839ac
--- /dev/null
+++ b/wqflask/utility/json/encoders.py
@@ -0,0 +1,17 @@
+"""Custom JSON encoders"""
+from uuid import UUID
+from json import JSONEncoder
+
+# Do not use this `__ENCODERS__` variable outside of this module.
+__ENCODERS__ = {
+    UUID: lambda obj: str(obj)
+}
+
+class CustomJSONEncoder(JSONEncoder):
+    """Custom JSONEncoder class."""
+    def default(self, obj):
+        """Serialise `obj` to a JSON representation."""
+        obj_type = type(obj)
+        if obj_type in __ENCODERS__:
+            return __ENCODERS__[obj_type](obj)
+        return JSONEncoder.default(self, obj)
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index d6751e3a..69732dfe 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -23,12 +23,15 @@ from flask import render_template
 from flask import request
 from flask import url_for
 
+from utility.json import CustomJSONEncoder
+
 from wqflask.database import database_connection
 from wqflask.decorators import login_required
 from wqflask.decorators import required_access
 from wqflask.decorators import edit_admins_access_required
 
 from wqflask.oauth2 import client
+from wqflask.oauth2 import session
 from wqflask.oauth2.request_utils import flash_error, process_error
 
 from gn3.authentication import AdminRole
@@ -123,6 +126,7 @@ def edit_probeset(conn, name):
 @metadata_edit.route("/<dataset_id>/traits/<name>")
 @required_access(
     ("group:resource:view-resource", "group:resource:edit-resource"))
+@login_required(pagename="phenotype edit")
 def display_phenotype_metadata(dataset_id: str, name: str):
     from utility.tools import get_setting
     with database_connection(get_setting("SQL_URI")) as conn:
@@ -167,15 +171,12 @@ def display_probeset_metadata(name: str):
 @metadata_edit.route("/<dataset_id>/traits/<name>", methods=("POST",))
 @required_access(
     ("group:resource:view-resource", "group:resource:edit-resource"))
+@login_required(pagename="phenotype update")
 def update_phenotype(dataset_id: str, name: str):
     from utility.tools import get_setting
     data_ = request.form.to_dict()
     TMPDIR = current_app.config.get("TMPDIR")
-    author = (
-        (g.user_session.record.get(b"user_id") or b"").decode("utf-8")
-        or g.user_session.record.get("user_id")
-        or ""
-    )
+    author = session.session_info()["user"]["user_id"]
     phenotype_id = str(data_.get("phenotype-id"))
     if not (file_ := request.files.get("file")) and data_.get('edited') == "false":
         flash("No sample-data has been uploaded", "warning")
@@ -272,7 +273,7 @@ def update_phenotype(dataset_id: str, name: str):
                     ),
                 }
             )
-            f.write(json.dumps(diff_data))
+            f.write(json.dumps(diff_data, cls=CustomJSONEncoder))
         url = url_for("metadata_edit.list_diffs")
         flash(f"Sample-data has been successfully uploaded.  \
 View the diffs <a href='{url}' target='_blank'>here</a>", "success")
-- 
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