diff options
Diffstat (limited to 'gn3/api/wiki.py')
| -rw-r--r-- | gn3/api/wiki.py | 75 |
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 |