From f0110a1cab4032d2f9fe7d3193178e9ec2383a68 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 16 Sep 2024 15:47:45 -0500
Subject: Fix minor bugs and linting and typing errors.

---
 uploader/oauth2/client.py                          |  2 +-
 uploader/session.py                                |  2 +-
 uploader/species/models.py                         | 28 ++++++++++++----------
 .../templates/populations/view-population.html     |  3 +++
 4 files changed, 20 insertions(+), 15 deletions(-)

(limited to 'uploader')

diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py
index e119cc3..70a32ff 100644
--- a/uploader/oauth2/client.py
+++ b/uploader/oauth2/client.py
@@ -61,7 +61,7 @@ def __update_auth_server_jwks__(jwks) -> KeySet:
 
 def auth_server_jwks() -> KeySet:
     """Fetch the auth-server JSON Web Keys information."""
-    _jwks = session.session_info().get("auth_server_jwks")
+    _jwks = session.session_info().get("auth_server_jwks") or {}
     if bool(_jwks):
         return __update_auth_server_jwks__({
             "last-updated": _jwks["last-updated"],
diff --git a/uploader/session.py b/uploader/session.py
index 399f28c..b538187 100644
--- a/uploader/session.py
+++ b/uploader/session.py
@@ -96,7 +96,7 @@ def user_token() -> Either:
 def set_auth_server_jwks(keyset: KeySet) -> KeySet:
     """Update the JSON Web Keys in the session."""
     save_session_info({
-        **session_info(),
+        **session_info(),# type: ignore[misc]
         "auth_server_jwks": {
             "last-updated": datetime.now().timestamp(),
             "jwks": keyset.as_dict()
diff --git a/uploader/species/models.py b/uploader/species/models.py
index 1abed6d..51f941c 100644
--- a/uploader/species/models.py
+++ b/uploader/species/models.py
@@ -28,7 +28,7 @@ def order_species_by_family(species: tuple[dict, ...]) -> list:
             **ordered,
             _key: ordered.get(_key, tuple()) + (current,)
         }
-    ordered = reduce(__order__, species, {})
+    ordered = reduce(__order__, species, {})# type: ignore[var-annotated]
     return sorted(tuple(ordered.items()), key=lambda item: item[0][0])
 
 
@@ -47,7 +47,7 @@ def save_species(conn: mdb.Connection,
                  common_name: str,
                  scientific_name: str,
                  family: str,
-                 taxon_id: Optional[str] = None) -> int:
+                 taxon_id: Optional[str] = None) -> dict:
     """
     Save a new species to the database.
 
@@ -58,14 +58,14 @@ def save_species(conn: mdb.Connection,
     common_name: The species' common name.
     scientific_name; The species' scientific name.
     """
-    genus, species = scientific_name.split(" ")
+    genus, species_name = scientific_name.split(" ")
     families = species_families(conn)
     with conn.cursor() as cursor:
         cursor.execute("SELECT MAX(OrderId) FROM Species")
         species = {
             "common_name": common_name,
             "common_name_lower": common_name.lower(),
-            "menu_name": f"{common_name} ({genus[0]}. {species.lower()})",
+            "menu_name": f"{common_name} ({genus[0]}. {species_name.lower()})",
             "scientific_name": scientific_name,
             "family": family,
             "family_order": families[family],
@@ -91,13 +91,15 @@ def save_species(conn: mdb.Connection,
         }
 
 
-def update_species(conn: mdb.Connection,
-                   species_id: int,
-                   common_name: str,
-                   scientific_name: str,
-                   family: str,
-                   family_order: int,
-                   species_order: int):
+def update_species(# pylint: disable=[too-many-arguments]
+        conn: mdb.Connection,
+        species_id: int,
+        common_name: str,
+        scientific_name: str,
+        family: str,
+        family_order: int,
+        species_order: int
+):
     """Update a species' details.
 
     Parameters
@@ -114,12 +116,12 @@ def update_species(conn: mdb.Connection,
     species_order: The ordering of this species in relation to others
     """
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        genus, species = scientific_name.split(" ")
+        genus, species_name = scientific_name.split(" ")
         species = {
             "species_id": species_id,
             "common_name": common_name,
             "common_name_lower": common_name.lower(),
-            "menu_name": f"{common_name} ({genus[0]}. {species.lower()})",
+            "menu_name": f"{common_name} ({genus[0]}. {species_name.lower()})",
             "scientific_name": scientific_name,
             "family": family,
             "family_order": family_order,
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 31db54f..319addc 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -23,6 +23,9 @@
 {%block contents%}
 <div class="row">
   <h2>Population Details</h2>
+
+  {{flash_all_messages()}}
+
   <dl>
     <dt>Name</dt>
     <dd>{{population.Name}}</dd>
-- 
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