8892829037

Committed 30 Apr 2024 09:55AM UTC coverage: 84.455%. First build

Build # 8892829037

Build Type

Pull #3148

github

Committed by

web-flow

Commit Message

Merge 8a772805d into 73c972545

Pull Request Pull Request #3148: add(create validation case)

Run Details

153 of 188 new or added lines in 6 files covered. (81.38%)

19776 of 23416 relevant lines covered (84.46%)

0.84 hits per line

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0.0

/cg/cli/validation.py

1	"""cg module for validation ofcases."""
2
NEW 3	import logging	×
NEW 4	from pathlib import Path	×
NEW 5	from typing import Tuple	×
6
NEW 7	import click	×
8
NEW 9	from cg.constants.constants import DRY_RUN	×
NEW 10	from cg.meta.create_validation_cases.validation_cases_api import CreateValidationCaseAPI	×
NEW 11	from cg.models.cg_config import CGConfig	×
12
NEW 13	LOG = logging.getLogger(__name__)	×
14
15
NEW 16	@click.group()	×
NEW 17	def validation():	×
18	"""Validate workflows."""
19
20
NEW 21	@validation.command("create-validation-case")	×
NEW 22	@click.option(	×
23	"-c",
24	"--case-id",
25	required=True,
26	help="Case identifier used in statusdb, e.g. supersonicturtle. The case information wil be transferred to the validation case.",
27	)
NEW 28	@click.option(	×
29	"-cn",
30	"--case-name",
31	required=True,
32	help="Case name that is used as name for the validation case.",
33	)
NEW 34	@click.option(	×
35	"-dv",
36	"--delivery",
37	required=False,
38	help="Delivery option for the validation case, if not set will take delivery option from original case.",
39	)
NEW 40	@click.option(	×
41	"-da",
42	"--data-analysis",
43	required=False,
44	help="Data analysis option for the validation case, if not set will take data analysis option from original case.",
45	)
NEW 46	@DRY_RUN	×
NEW 47	@click.pass_obj	×
NEW 48	def create_validation_case(	×
49	context: CGConfig, case_id: str, case_name: str, delivery: str, data_analysis: str
50	):
51	"""Create a validation case to be used in workflow validation."""
NEW 52	validation_case_api = CreateValidationCaseAPI(	×
53	status_db=context.status_db, housekeeper_api=context.housekeeper_api
54	)
55
NEW 56	try:	×
NEW 57	validation_case_api.create_validation_case(	×
58	case_id=case_id, case_name=case_name, delivery=delivery, data_analysis=data_analysis
59	)
NEW 60	except Exception as error:	×
NEW 61	LOG.error(f"An error occured {repr(error)}.")	×
NEW 62	raise click.Abort	×

Clinical-Genomics / cg / 8892829037

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