10418406160

Committed 16 Aug 2024 10:18AM UTC coverage: 89.736%. First build

Build # 10418406160

Build Type

Pull #474

github

Committed by

seallard

Commit Message

Fix imports

Pull Request Pull Request #474: Add endpoint error handling

Run Details

60 of 79 new or added lines in 2 files covered. (75.95%)

2177 of 2426 relevant lines covered (89.74%)

0.9 hits per line

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80.0

/trailblazer/server/utils.py

import datetime
from http import HTTPStatus
from flask import Request, jsonify
import logging
from functools import wraps
from pydantic import ValidationError

from trailblazer.exc import MissingAnalysis
from trailblazer.dto import AnalysesRequest
from trailblazer.services.authentication_service.exceptions import AuthenticationError

LOG = logging.getLogger(__name__)

def parse_analyses_request(request: Request) -> AnalysesRequest:
    """Parse a request for retrieving analyses."""
    query_params = {}
    for key in request.args.keys():
        if key_has_list_of_values(key):
            query_params[key[:-2]] = request.args.getlist(key)
        else:
            query_params[key] = request.args.get(key)
    return AnalysesRequest.model_validate(query_params)


def key_has_list_of_values(key: str) -> bool:
    return key.endswith("[]")


def stringify_timestamps(data: dict) -> dict[str, str]:
    """Convert datetime into string before dumping in order to avoid information loss"""
    for key, val in data.items():
        if isinstance(val, datetime.datetime):
            data[key] = str(val)
    return data


def handle_endpoint_errors(func):

    @wraps(func)
    def wrapper(*args, **kwargs):
        try:
            return func(*args, **kwargs)
        except AuthenticationError:
            return jsonify("User not allowed"), HTTPStatus.FORBIDDEN
        except MissingAnalysis as error:
            return jsonify(error=str(error)), HTTPStatus.NOT_FOUND
        except ValidationError as error:
            LOG.error(f"Validation error in analysis endpoint: {error}")
            return jsonify(error=str(error)), HTTPStatus.BAD_REQUEST
        except Exception as error:
            LOG.error(f"Unexpected error in analysis endpoint: {error}")
            return (
                jsonify(error="An error occurred while processing your request."),
                HTTPStatus.INTERNAL_SERVER_ERROR,
            )

    return wrapper

1	import datetime	1✔
2	from http import HTTPStatus	1✔
3	from flask import Request, jsonify	1✔
4	import logging	1✔
5	from functools import wraps	1✔
6	from pydantic import ValidationError	1✔
7
8	from trailblazer.exc import MissingAnalysis	1✔
9	from trailblazer.dto import AnalysesRequest	1✔
10	from trailblazer.services.authentication_service.exceptions import AuthenticationError	1✔
11
12	LOG = logging.getLogger(__name__)	1✔
13
14	def parse_analyses_request(request: Request) -> AnalysesRequest:	1✔
15	"""Parse a request for retrieving analyses."""
16	query_params = {}	1✔
17	for key in request.args.keys():	1✔
18	if key_has_list_of_values(key):	1✔
19	query_params[key[:-2]] = request.args.getlist(key)	1✔
20	else:
21	query_params[key] = request.args.get(key)	1✔
22	return AnalysesRequest.model_validate(query_params)	1✔
23
24
25	def key_has_list_of_values(key: str) -> bool:	1✔
26	return key.endswith("[]")	1✔
27
28
29	def stringify_timestamps(data: dict) -> dict[str, str]:	1✔
30	"""Convert datetime into string before dumping in order to avoid information loss"""
31	for key, val in data.items():	×
32	if isinstance(val, datetime.datetime):	×
33	data[key] = str(val)	×
34	return data	×
35
36
37	def handle_endpoint_errors(func):	1✔
38
39	@wraps(func)	1✔
40	def wrapper(args, *kwargs):	1✔
41	try:	1✔
42	return func(args, *kwargs)	1✔
43	except AuthenticationError:	1✔
NEW 44	return jsonify("User not allowed"), HTTPStatus.FORBIDDEN	×
45	except MissingAnalysis as error:	1✔
46	return jsonify(error=str(error)), HTTPStatus.NOT_FOUND	1✔
47	except ValidationError as error:	1✔
48	LOG.error(f"Validation error in analysis endpoint: {error}")	1✔
49	return jsonify(error=str(error)), HTTPStatus.BAD_REQUEST	1✔
NEW 50	except Exception as error:	×
NEW 51	LOG.error(f"Unexpected error in analysis endpoint: {error}")	×
NEW 52	return (	×
53	jsonify(error="An error occurred while processing your request."),
54	HTTPStatus.INTERNAL_SERVER_ERROR,
55	)
56
57	return wrapper	1✔

Clinical-Genomics / trailblazer / 10418406160

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