diff options
| -rw-r--r-- | gn3/api/metadata.py | 3 | ||||
| -rw-r--r-- | gn3/api/metadata_api/wiki.py (renamed from gn3/api/wiki.py) | 44 | ||||
| -rw-r--r-- | gn3/db/wiki.py | 38 |
3 files changed, 47 insertions, 38 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 9d82dba..53daf67 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -18,6 +18,8 @@ from gn3.db.rdf import RDF_PREFIXES from gn3.db.rdf import (query_frame_and_compact, query_and_compact) +from gn3.api.metadata_api import wiki + BASE_CONTEXT = { "data": "@graph", @@ -142,6 +144,7 @@ PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | { } metadata = Blueprint("metadata", __name__) +metadata.register_blueprint(wiki.wiki_blueprint) @metadata.route("/datasets/<name>", methods=["GET"]) diff --git a/gn3/api/wiki.py b/gn3/api/metadata_api/wiki.py index 2b8369f..7e22c94 100644 --- a/gn3/api/wiki.py +++ b/gn3/api/metadata_api/wiki.py @@ -2,16 +2,17 @@ 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("wiki", __name__) +wiki_blueprint = Blueprint("wiki", __name__, url_prefix="wiki") class MissingDBDataException(Exception): pass -@wiki.route("/<int:comment_id>/edit", methods=["POST"]) +@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 @@ -40,9 +41,9 @@ def edit_wiki(comment_id: int): with db_utils.database_connection(current_app.config["SQL_URI"]) as conn: cursor = conn.cursor() 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) + 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 @@ -58,36 +59,3 @@ def edit_wiki(comment_id: int): ) return jsonify({"success": "ok"}) return jsonify(error="Error editting wiki entry, most likely due to DB error!"), 500 - - -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() - 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 diff --git a/gn3/db/wiki.py b/gn3/db/wiki.py new file mode 100644 index 0000000..a56f26c --- /dev/null +++ b/gn3/db/wiki.py @@ -0,0 +1,38 @@ +from typing import List + + +class MissingDBDataException(Exception): + pass + + +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() + 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 |