10490912680

Committed 21 Aug 2024 01:29PM UTC coverage: 88.118% (-0.2%) from 88.353%

Build # 10490912680

Build Type

push

github

Committed by

web-flow

Commit Message

Add cancel endpoint (#475)

Run Details

15 of 23 new or added lines in 5 files covered. (65.22%)

2084 of 2365 relevant lines covered (88.12%)

0.88 hits per line

Source File
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78.57

/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 CancelSlurmAnalysisNotSupportedError, 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 CancelSlurmAnalysisNotSupportedError as error:
            return jsonify(error=str(error)), HTTPStatus.BAD_REQUEST
        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 CancelSlurmAnalysisNotSupportedError, 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
15	def parse_analyses_request(request: Request) -> AnalysesRequest:	1✔
16	"""Parse a request for retrieving analyses."""
17	query_params = {}	1✔
18	for key in request.args.keys():	1✔
19	if key_has_list_of_values(key):	1✔
20	query_params[key[:-2]] = request.args.getlist(key)	1✔
21	else:
22	query_params[key] = request.args.get(key)	1✔
23	return AnalysesRequest.model_validate(query_params)	1✔
24
25
26	def key_has_list_of_values(key: str) -> bool:	1✔
27	return key.endswith("[]")	1✔
28
29
30	def stringify_timestamps(data: dict) -> dict[str, str]:	1✔
31	"""Convert datetime into string before dumping in order to avoid information loss"""
32	for key, val in data.items():	×
33	if isinstance(val, datetime.datetime):	×
34	data[key] = str(val)	×
35	return data	×
36
37
38	def handle_endpoint_errors(func):	1✔
39
40	@wraps(func)	1✔
41	def wrapper(args, *kwargs):	1✔
42	try:	1✔
43	return func(args, *kwargs)	1✔
44	except AuthenticationError:	1✔
45	return jsonify("User not allowed"), HTTPStatus.FORBIDDEN	×
46	except MissingAnalysis as error:	1✔
47	return jsonify(error=str(error)), HTTPStatus.NOT_FOUND	1✔
48	except CancelSlurmAnalysisNotSupportedError as error:	1✔
NEW 49	return jsonify(error=str(error)), HTTPStatus.BAD_REQUEST	×
50	except ValidationError as error:	1✔
51	LOG.error(f"Validation error in analysis endpoint: {error}")	1✔
52	return jsonify(error=str(error)), HTTPStatus.BAD_REQUEST	1✔
53	except Exception as error:	×
54	LOG.error(f"Unexpected error in analysis endpoint: {error}")	×
55	return (	×
56	jsonify(error="An error occurred while processing your request."),
57	HTTPStatus.INTERNAL_SERVER_ERROR,
58	)
59
60	return wrapper	1✔

Clinical-Genomics / trailblazer / 10490912680

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