From 7b2a1794c1b7e7c589b1abe6d307b2a7e4cd2c42 Mon Sep 17 00:00:00 2001
From: John Nduli
Date: Mon, 26 Aug 2024 12:40:15 +0300
Subject: refactor: split out utlities into their modules and change api to use
 metadata

---
 gn3/api/metadata_api/wiki.py | 61 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 gn3/api/metadata_api/wiki.py

(limited to 'gn3/api/metadata_api/wiki.py')

diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
new file mode 100644
index 0000000..7e22c94
--- /dev/null
+++ b/gn3/api/metadata_api/wiki.py
@@ -0,0 +1,61 @@
+import datetime
+from typing import Any, Dict, List
+from flask import Blueprint, request, jsonify, current_app
+from gn3 import db_utils
+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):
+    # 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", [])]
+
+    insert_dict = {
+        "Id": comment_id,
+        "symbol": payload["symbol"],
+        "PubMed_ID": " ".join(pubmed_ids),
+        "comment": payload["comment"],
+        "email": payload["email"],
+        "createtime": datetime.datetime.now(datetime.timezone.utc).strftime(
+            "%Y-%m-%d %H:%M"
+        ),
+        "user_ip": request.environ.get("HTTP_X_REAL_IP", request.remote_addr),
+        "weburl": payload.get("web_url"),
+        "initial": payload.get("initial"),
+        "reason": payload["reason"],
+    }
+
+    insert_query = """
+    INSERT INTO GeneRIF (Id, versionId, symbol, PubMed_ID, SpeciesID, comment,
+                         email, createtime, user_ip, weburl, initial, reason)
+    VALUES (%(Id)s, %(versionId)s, %(symbol)s, %(PubMed_ID)s, %(SpeciesID)s, %(comment)s, %(email)s, %(createtime)s, %(user_ip)s, %(weburl)s, %(initial)s, %(reason)s)
+    """
+    with db_utils.database_connection(current_app.config["SQL_URI"]) as conn:
+        cursor = conn.cursor()
+        try:
+            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:
+            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)"
+
+        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
-- 
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