diff options
Diffstat (limited to 'gn3/api/metadata_api')
| -rw-r--r-- | gn3/api/metadata_api/wiki.py | 80 |
1 files changed, 71 insertions, 9 deletions
diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py index 8df6cfb..70c5cf4 100644 --- a/gn3/api/metadata_api/wiki.py +++ b/gn3/api/metadata_api/wiki.py @@ -1,27 +1,31 @@ -"""API for accessing/editting wiki metadata""" +"""API for accessing/editing rif/wiki metadata""" import datetime from typing import Any, Dict +from typing import Optional from flask import Blueprint, request, jsonify, current_app, make_response from gn3 import db_utils -from gn3.auth.authorisation.oauth2.resource_server import require_oauth +from gn3.oauth2.authorisation import require_token from gn3.db import wiki from gn3.db.rdf.wiki import ( get_wiki_entries_by_symbol, get_comment_history, update_wiki_comment, + get_rif_entries_by_symbol, + delete_wiki_entries_by_id, ) wiki_blueprint = Blueprint("wiki", __name__, url_prefix="wiki") +rif_blueprint = Blueprint("rif", __name__, url_prefix="rif") +@wiki_blueprint.route("/edit", methods=["POST"], defaults={'comment_id': None}) @wiki_blueprint.route("/<int:comment_id>/edit", methods=["POST"]) -@require_oauth("profile") -def edit_wiki(comment_id: int): - """Edit wiki comment. This is achieved by adding another entry with a new VersionId""" +def edit_wiki(comment_id: Optional[int]): + """Edit/Insert 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 # type: ignore pubmed_ids = [str(x) for x in payload.get("pubmed_ids", [])] @@ -48,13 +52,17 @@ def edit_wiki(comment_id: int): 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() - next_version = 0 + cursor, next_version = conn.cursor(), 0 + if not comment_id: + comment_id = wiki.get_next_comment_id(cursor) + insert_dict["Id"] = comment_id + else: + next_version = wiki.get_next_comment_version(cursor, comment_id) + 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 wiki.MissingDBDataException as missing_exc: return jsonify(error=f"Error editing wiki entry, {missing_exc}"), 500 insert_dict["SpeciesID"] = species_id @@ -83,7 +91,7 @@ def edit_wiki(comment_id: int): sparql_auth_uri=current_app.config["SPARQL_AUTH_URI"] ) except Exception as exc: - conn.rollback() # type: ignore + conn.rollback() # type: ignore raise exc return jsonify({"success": "ok"}) return jsonify(error="Error editing wiki entry, most likely due to DB error!"), 500 @@ -154,3 +162,57 @@ def get_history(comment_id): payload.headers["Content-Type"] = "application/ld+json" return payload, status_code return jsonify(data), status_code + + +@rif_blueprint.route("/<string:symbol>", methods=["GET"]) +def get_ncbi_rif_entries(symbol: str): + """Fetch NCBI RIF entries""" + status_code = 200 + response = get_rif_entries_by_symbol( + symbol, + sparql_uri=current_app.config["SPARQL_ENDPOINT"]) + data = response.get("data") + if not data: + data, status_code = {}, 404 + if request.headers.get("Accept") == "application/ld+json": + payload = make_response(response) + payload.headers["Content-Type"] = "application/ld+json" + return payload, status_code + return jsonify(data), status_code + + +@wiki_blueprint.route("/delete", methods=["POST"], defaults={'comment_id': None}) +@wiki_blueprint.route("/<int:comment_id>/delete", methods=["POST"]) +@require_token +def delete_wiki(comment_id: Optional[int] = None, **kwargs): # pylint: disable=[unused-argument] + """Delete a wiki entry by its comment_id from both SQL and RDF.""" + if comment_id is None: + return jsonify(error="comment_id is required for deletion."), 400 + with (db_utils.database_connection(current_app.config["SQL_URI"]) as conn, + conn.cursor() as cursor): + try: + # Delete from SQL + delete_query = "DELETE FROM GeneRIF WHERE Id = %s" + current_app.logger.debug( + f"Running query: {delete_query} with Id={comment_id}") + cursor.execute(delete_query, (comment_id,)) + # Delete from RDF + try: + delete_wiki_entries_by_id( + wiki_id=comment_id, + sparql_user=current_app.config["SPARQL_USER"], + sparql_password=current_app.config["SPARQL_PASSWORD"], + sparql_auth_uri=current_app.config["SPARQL_AUTH_URI"], + graph="<http://genenetwork.org>" + ) + # pylint: disable=W0718 + except Exception as rdf_exc: + current_app.logger.error(f"RDF deletion failed: {rdf_exc}") + conn.rollback() + return jsonify(error="Failed to delete wiki entry from RDF store."), 500 + return jsonify({"success": "Wiki entry deleted successfully."}), 200 + # pylint: disable=W0718 + except Exception as exc: + conn.rollback() + current_app.logger.error(f"Error deleting wiki entry: {exc}") + return jsonify(error="Error deleting wiki entry, most likely due to DB error!"), 500 |