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-rw-r--r--gn3/api/wiki.py75
1 files changed, 48 insertions, 27 deletions
diff --git a/gn3/api/wiki.py b/gn3/api/wiki.py
index f96a3dc..2b8369f 100644
--- a/gn3/api/wiki.py
+++ b/gn3/api/wiki.py
@@ -1,14 +1,20 @@
import datetime
+from typing import Any, Dict, List
from flask import Blueprint, request, jsonify, current_app
from gn3 import db_utils
+
wiki = Blueprint("wiki", __name__)
-@wiki.route("/comments/<int:comment_id>/edit", methods=["POST"])
+class MissingDBDataException(Exception):
+ pass
+
+
+@wiki.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 = request.json
+ payload: Dict[str, Any] = request.json
pubmed_ids = [str(x) for x in payload.get("pubmed_ids", [])]
insert_dict = {
@@ -16,10 +22,7 @@ def edit_wiki(comment_id: int):
"symbol": payload["symbol"],
"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
"email": payload["email"],
- # DB doesn't default to now
"createtime": datetime.datetime.now(datetime.timezone.utc).strftime(
"%Y-%m-%d %H:%M"
),
@@ -36,37 +39,55 @@ def edit_wiki(comment_id: int):
"""
with db_utils.database_connection(current_app.config["SQL_URI"]) as conn:
cursor = conn.cursor()
- 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
+ try:
+ category_ids = get_categories_ids(cursor, payload["categories"])
+ species_id = get_species_id(cursor, payload["species"])
+ next_version = 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))
+ 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:
+def get_species_id(cursor, species_name: str) -> int:
+ cursor.execute("SELECT SpeciesID from Species WHERE Name = %s", (species_name,))
+ species_ids = cursor.fetchall()
+ if len(species_ids) != 1:
+ raise MissingDBDataException(
+ f"expected 1 species with Name={species_name} but found {len(species_ids)}!"
+ )
+ return species_ids[0][0]
+
+
+def get_next_comment_version(cursor, comment_id: int) -> int:
+ 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:
+ raise MissingDBDataException(f"No comment found with comment_id={comment_id}")
+ return latest_version + 1
+
+
+def get_categories_ids(cursor, categories: List[str]) -> List[int]:
cursor.execute("SELECT Name, Id from GeneCategory")
raw_categories = cursor.fetchall()
- return dict(raw_categories)
+ dict_cats = dict(raw_categories)
+ category_ids = []
+ for category in set(categories):
+ cat_id = dict_cats.get(category.strip())
+ if cat_id is None:
+ raise MissingDBDataException(f"Category with Name={category} not found")
+ category_ids.append(cat_id)
+ return category_ids