chore: fix pylint errors

2 files changed, 15 insertions, 8 deletions

diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
index 7e22c94..dc131d3 100644
--- a/gn3/api/metadata_api/wiki.py
+++ b/gn3/api/metadata_api/wiki.py
@@ -1,5 +1,7 @@
+"""API for accessing/editting wiki metadata"""
+
 import datetime
-from typing import Any, Dict, List
+from typing import Any, Dict
 from flask import Blueprint, request, jsonify, current_app
 from gn3 import db_utils
 from gn3.db import wiki
@@ -8,12 +10,9 @@ from gn3.db import wiki
 wiki_blueprint = Blueprint("wiki", __name__, url_prefix="wiki")
 
 
-class MissingDBDataException(Exception):
-    pass
-
-
 @wiki_blueprint.route("/<int:comment_id>/edit", methods=["POST"])
 def edit_wiki(comment_id: int):
+    """Edit wiki comment. This is achieved by adding another entry with a new VersionId"""
     # FIXME: attempt to check and fix for types here with relevant errors
     payload: Dict[str, Any] = request.json
     pubmed_ids = [str(x) for x in payload.get("pubmed_ids", [])]
@@ -44,13 +43,16 @@ def edit_wiki(comment_id: int):
             category_ids = wiki.get_categories_ids(cursor, payload["categories"])
             species_id = wiki.get_species_id(cursor, payload["species"])
             next_version = wiki.get_next_comment_version(cursor, comment_id)
-        except MissingDBDataException as missing_exc:
+        except wiki.MissingDBDataException as missing_exc:
             return jsonify(error=f"Error editting wiki entry, {missing_exc}"), 500
         insert_dict["SpeciesID"] = species_id
         insert_dict["versionId"] = next_version
         current_app.logger.debug(f"Running query: {insert_query}")
         cursor.execute(insert_query, insert_dict)
-        category_addition_query = "INSERT INTO GeneRIFXRef (GeneRIFId, versionId, GeneCategoryId) VALUES (%s, %s, %s)"
+        category_addition_query = """
+            INSERT INTO GeneRIFXRef (GeneRIFId, versionId, GeneCategoryId)
+                VALUES (%s, %s, %s)
+            """
 
         for cat_id in category_ids:
             current_app.logger.debug(f"Running query: {category_addition_query}")
diff --git a/gn3/db/wiki.py b/gn3/db/wiki.py
index a56f26c..c3cfee0 100644
--- a/gn3/db/wiki.py
+++ b/gn3/db/wiki.py
@@ -1,11 +1,14 @@
+"""Helper functions to access wiki entries"""
+
 from typing import List
 
 
 class MissingDBDataException(Exception):
-    pass
+    """Error due to DB missing some data"""
 
 
 def get_species_id(cursor, species_name: str) -> int:
+    """Find species id given species `Name`"""
     cursor.execute("SELECT SpeciesID from Species  WHERE Name = %s", (species_name,))
     species_ids = cursor.fetchall()
     if len(species_ids) != 1:
@@ -16,6 +19,7 @@ def get_species_id(cursor, species_name: str) -> int:
 
 
 def get_next_comment_version(cursor, comment_id: int) -> int:
+    """Find the version to add, usually latest_version + 1"""
     cursor.execute(
         "SELECT MAX(versionId) as version_id from GeneRIF WHERE Id = %s", (comment_id,)
     )
@@ -26,6 +30,7 @@ def get_next_comment_version(cursor, comment_id: int) -> int:
 
 
 def get_categories_ids(cursor, categories: List[str]) -> List[int]:
+    """Get the categories_ids from a list of category strings"""
     cursor.execute("SELECT Name, Id from GeneCategory")
     raw_categories = cursor.fetchall()
     dict_cats = dict(raw_categories)