8920038569

Committed 02 May 2024 07:13AM UTC coverage: 84.527%. First build

Build # 8920038569

Build Type

Pull #3148

github

Committed by

web-flow

Commit Message

Merge a6d83dc9b into 73c972545

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

Run Details

174 of 193 new or added lines in 7 files covered. (90.16%)

19797 of 23421 relevant lines covered (84.53%)

0.85 hits per line

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75.0

/cg/cli/validation.py

"""cg module for validation ofcases."""

import logging
from pathlib import Path
from typing import Tuple

import click

from cg.constants.constants import DRY_RUN
from cg.meta.create_validation_cases.validation_cases_api import CreateValidationCaseAPI
from cg.models.cg_config import CGConfig

LOG = logging.getLogger(__name__)


@click.group()
def validation():
    """Validate workflows."""


@validation.command("create-validation-case")
@click.option(
    "-c",
    "--case-id",
    required=True,
    help="Case identifier used in statusdb, e.g. supersonicturtle. The case information wil be transferred to the validation case.",
)
@click.option(
    "-cn",
    "--case-name",
    required=True,
    help="Case name that is used as name for the validation case.",
)
@click.option(
    "-dv",
    "--delivery",
    required=False,
    help="Delivery option for the validation case, if not set will take delivery option from original case.",
)
@click.option(
    "-da",
    "--data-analysis",
    required=False,
    help="Data analysis option for the validation case, if not set will take data analysis option from original case.",
)
@DRY_RUN
@click.pass_obj
def create_validation_case(
    context: CGConfig,
    case_id: str,
    case_name: str,
    delivery: str,
    data_analysis: str,
    dry_run: bool,
):
    """Create a validation case to be used in workflow validation."""
    validation_case_api = CreateValidationCaseAPI(
        status_db=context.status_db, housekeeper_api=context.housekeeper_api
    )

    try:
        validation_case_api.create_validation_case(
            case_id=case_id,
            case_name=case_name,
            delivery=delivery,
            data_analysis=data_analysis,
            dry_run=dry_run,
        )
    except Exception as error:
        LOG.error(f"An error occured {repr(error)}.")
        raise click.Abort

1	"""cg module for validation ofcases."""
2
3	import logging	1✔
4	from pathlib import Path	1✔
5	from typing import Tuple	1✔
6
7	import click	1✔
8
9	from cg.constants.constants import DRY_RUN	1✔
10	from cg.meta.create_validation_cases.validation_cases_api import CreateValidationCaseAPI	1✔
11	from cg.models.cg_config import CGConfig	1✔
12
13	LOG = logging.getLogger(__name__)	1✔
14
15
16	@click.group()	1✔
17	def validation():	1✔
18	"""Validate workflows."""
19
20
21	@validation.command("create-validation-case")	1✔
22	@click.option(	1✔
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	)
28	@click.option(	1✔
29	"-cn",
30	"--case-name",
31	required=True,
32	help="Case name that is used as name for the validation case.",
33	)
34	@click.option(	1✔
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	)
40	@click.option(	1✔
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	)
46	@DRY_RUN	1✔
47	@click.pass_obj	1✔
48	def create_validation_case(	1✔
49	context: CGConfig,
50	case_id: str,
51	case_name: str,
52	delivery: str,
53	data_analysis: str,
54	dry_run: bool,
55	):
56	"""Create a validation case to be used in workflow validation."""
NEW 57	validation_case_api = CreateValidationCaseAPI(	×
58	status_db=context.status_db, housekeeper_api=context.housekeeper_api
59	)
60
NEW 61	try:	×
NEW 62	validation_case_api.create_validation_case(	×
63	case_id=case_id,
64	case_name=case_name,
65	delivery=delivery,
66	data_analysis=data_analysis,
67	dry_run=dry_run,
68	)
NEW 69	except Exception as error:	×
NEW 70	LOG.error(f"An error occured {repr(error)}.")	×
NEW 71	raise click.Abort	×

Clinical-Genomics / cg / 8920038569

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