15825966872

Committed 23 Jun 2025 01:43PM UTC coverage: 85.746%. First build

Build # 15825966872

Build Type

Pull #4455

github

Committed by

web-flow

Commit Message

Merge 5a141a96b into 0a466245f

Pull Request Pull Request #4455: fix completed at before started at in analysis table

Run Details

51 of 60 new or added lines in 14 files covered. (85.0%)

26672 of 31106 relevant lines covered (85.75%)

0.86 hits per line

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52.63

/cg/cli/upload/coverage.py

"""Code for uploading coverage reports via CLI"""

import rich_click as click

from cg.meta.upload.coverage import UploadCoverageApi
from cg.models.cg_config import CGConfig
from cg.store.models import Case
from cg.store.store import Store

from .utils import suggest_cases_to_upload


@click.command("coverage")
@click.argument("family_id", required=False)
@click.pass_obj
def upload_coverage(context: CGConfig, family_id):
    """Upload coverage from an analysis to Chanjo."""

    click.echo(click.style("----------------- COVERAGE --------------------"))

    status_db: Store = context.status_db

    if not family_id:
        suggest_cases_to_upload(status_db=status_db)
        raise click.Abort

    case: Case = status_db.get_case_by_internal_id(internal_id=family_id)
    upload_coverage_api = UploadCoverageApi(
        status_api=status_db,
        hk_api=context.housekeeper_api,
        chanjo_api=context.chanjo_api,
    )
    coverage_data = upload_coverage_api.data(case.latest_analysis)
    upload_coverage_api.upload(coverage_data)

1	"""Code for uploading coverage reports via CLI"""
2
3	import rich_click as click	1✔
4
5	from cg.meta.upload.coverage import UploadCoverageApi	1✔
6	from cg.models.cg_config import CGConfig	1✔
7	from cg.store.models import Case	1✔
8	from cg.store.store import Store	1✔
9
10	from .utils import suggest_cases_to_upload	1✔
11
12
13	@click.command("coverage")	1✔
14	@click.argument("family_id", required=False)	1✔
15	@click.pass_obj	1✔
16	def upload_coverage(context: CGConfig, family_id):	1✔
17	"""Upload coverage from an analysis to Chanjo."""
18
19	click.echo(click.style("----------------- COVERAGE --------------------"))	×
20
21	status_db: Store = context.status_db	×
22
23	if not family_id:	×
24	suggest_cases_to_upload(status_db=status_db)	×
25	raise click.Abort	×
26
NEW 27	case: Case = status_db.get_case_by_internal_id(internal_id=family_id)	×
28	upload_coverage_api = UploadCoverageApi(	×
29	status_api=status_db,
30	hk_api=context.housekeeper_api,
31	chanjo_api=context.chanjo_api,
32	)
NEW 33	coverage_data = upload_coverage_api.data(case.latest_analysis)	×
34	upload_coverage_api.upload(coverage_data)	×

Clinical-Genomics / cg / 15825966872

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