feat: add support for categories in edit query and clearer errors

1 files changed, 35 insertions, 14 deletions

diff --git a/gn3/api/wiki.py b/gn3/api/wiki.py
index 133d7c8..f96a3dc 100644
--- a/gn3/api/wiki.py
+++ b/gn3/api/wiki.py
@@ -7,13 +7,14 @@ wiki = Blueprint("wiki", __name__)
 
 @wiki.route("/comments/<int:comment_id>/edit", methods=["POST"])
 def edit_wiki(comment_id: int):
+    # FIXME: attempt to check and fix for types here with relevant errors
     payload = request.json
+    pubmed_ids = [str(x) for x in payload.get("pubmed_ids", [])]
+
     insert_dict = {
         "Id": comment_id,
-        "versionId": payload["version_id"],
         "symbol": payload["symbol"],
-        "PubMed_ID": payload.get("pubmed_id"),
-        "SpeciesID": payload["species_id"],
+        "PubMed_ID": " ".join(pubmed_ids),
         "comment": payload["comment"],
         # does this need to be part of the payload or can we get this from session information
         # e.g. https://github.com/genenetwork/genenetwork2/blob/0998033d0a7ea26ed96b00a360a334bae6de8c55/gn2/wqflask/oauth2/session.py#L22-L23
@@ -28,15 +29,6 @@ def edit_wiki(comment_id: int):
         "reason": payload["reason"],
     }
 
-    if not isinstance(insert_dict["versionId"], int):
-        return jsonify(
-            error=f"Error editting wiki entry, expected versionId as int but got {insert_dict['versionId']}!"
-        ), 500
-    if not isinstance(insert_dict["SpeciesID"], int):
-        return jsonify(
-            error=f"Error editting wiki entry, expected versionId as int but got {insert_dict['SpeciesID']}!"
-        ), 500
-
     insert_query = """
     INSERT INTO GeneRIF (Id, versionId, symbol, PubMed_ID, SpeciesID, comment,
                          email, createtime, user_ip, weburl, initial, reason)
@@ -44,8 +36,37 @@ def edit_wiki(comment_id: int):
     """
     with db_utils.database_connection(current_app.config["SQL_URI"]) as conn:
         cursor = conn.cursor()
-        current_app.logger.error(f"Inserting: {insert_dict}")
-        current_app.logger.error(f"wiht query: {insert_query}")
+        categories = get_categories(cursor)
+        category_ids = []
+        for category in payload["categories"]:
+            cat_id = categories.get(category.strip())
+            if cat_id is None:
+                return jsonify(error=f"Error editting wiki entry, category with Name={category} not found"), 500
+            category_ids.append(cat_id)
+        cursor.execute("SELECT SpeciesID from Species  WHERE Name = %s", (payload["species"],))
+        species_ids = cursor.fetchall()
+        if len(species_ids) != 1:
+            return jsonify(error=f"Error editting wiki entry, expected 1 species with Name={payload['species']} but found {len(species_ids)}!"), 500
+        insert_dict["SpeciesID"] = species_ids[0][0]
+
+        cursor.execute("SELECT MAX(versionId) as version_id from GeneRIF WHERE Id = %s", (comment_id,))
+        latest_version = cursor.fetchone()[0]
+        if latest_version is None:
+            return jsonify(error=f"Error editting wiki entry, No comments found with comment_id={comment_id}"), 500
+        insert_dict["versionId"] = latest_version + 1
+        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)"
+
+        for cat_id in category_ids:
+            current_app.logger.debug(f"Running query: {category_addition_query}")
+            cursor.execute(category_addition_query, (comment_id, insert_dict["versionId"], cat_id))
         return jsonify({"success": "ok"})
     return jsonify(error="Error editting wiki entry, most likely due to DB error!"), 500
+
+
+def get_categories(cursor) -> dict:
+    cursor.execute("SELECT Name, Id from GeneCategory")
+    raw_categories = cursor.fetchall()
+    return dict(raw_categories)