15705278932

Committed 17 Jun 2025 10:53AM UTC coverage: 100.0%. First build

Build # 15705278932

Build Type

Pull #4450

github

Committed by

web-flow

Commit Message

Merge c45efc7b0 into de46eeb46

Pull Request Pull Request #4450: fix nextflow store available

Run Details

9 of 26 new or added lines in 5 files covered. (34.62%)

0 of 0 relevant lines covered (NaN%)

0.0 hits per line

Source File
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61.36

/cg/cli/workflow/raw_data/base.py

import logging

import rich_click as click

from cg.cli.utils import CLICK_CONTEXT_SETTINGS
from cg.cli.workflow.commands import ARGUMENT_CASE_ID
from cg.cli.workflow.raw_data.raw_data_service import RawDataAnalysisService
from cg.constants.cli_options import DRY_RUN
from cg.constants.constants import Workflow
from cg.meta.workflow.analysis import AnalysisAPI
from cg.services.sequencing_qc_service import SequencingQCService
from cg.store.store import Store

LOG = logging.getLogger(__name__)


@click.group(invoke_without_command=True, context_settings=CLICK_CONTEXT_SETTINGS)
@click.pass_context
def raw_data(context: click.Context):
    """Function for storing raw-data-cases"""
    AnalysisAPI.get_help(context)


@raw_data.command("store")
@DRY_RUN
@ARGUMENT_CASE_ID
@click.pass_context
def store_raw_data_analysis(context: click.Context, case_id: str, dry_run: bool = False):
    LOG.info(f"Creating an analysis for case {case_id}")

    if dry_run:
        return

    raw_data_service = RawDataAnalysisService(
        store=context.obj.status_db,
        trailblazer_api=context.obj.trailblazer_api,
    )
    raw_data_service.store_analysis(case_id)


@raw_data.command("store-available")
@DRY_RUN
@click.pass_context
def store_available_raw_data_analysis(context: click.Context, dry_run: bool = False):
    """Creates an analysis object in status-db for all raw data cases to be delivered."""
    status_db: Store = context.obj.status_db
    was_successful: bool = True
    for case in status_db.get_cases_to_analyze(workflow=Workflow.RAW_DATA):
        LOG.info(f"Creating an analysis for case {case.internal_id}")
        if SequencingQCService.case_pass_sequencing_qc(case):
            if dry_run:
                return
            try:
                raw_data_service = RawDataAnalysisService(
                    store=context.obj.status_db,
                    trailblazer_api=context.obj.trailblazer_api,
                )
                raw_data_service.store_analysis(case.internal_id)
            except Exception as error:
                LOG.error(f"Failed to store analysis for case {case.internal_id}: {error}")
                was_successful = False
    if not was_successful:
        raise click.Abort()

1	import logging	1✔
2
3	import rich_click as click	1✔
4
5	from cg.cli.utils import CLICK_CONTEXT_SETTINGS	1✔
6	from cg.cli.workflow.commands import ARGUMENT_CASE_ID	1✔
7	from cg.cli.workflow.raw_data.raw_data_service import RawDataAnalysisService	1✔
8	from cg.constants.cli_options import DRY_RUN	1✔
9	from cg.constants.constants import Workflow	1✔
10	from cg.meta.workflow.analysis import AnalysisAPI	1✔
11	from cg.services.sequencing_qc_service import SequencingQCService	1✔
12	from cg.store.store import Store	1✔
13
14	LOG = logging.getLogger(__name__)	1✔
15
16
17	@click.group(invoke_without_command=True, context_settings=CLICK_CONTEXT_SETTINGS)	1✔
18	@click.pass_context	1✔
19	def raw_data(context: click.Context):	1✔
20	"""Function for storing raw-data-cases"""
21	AnalysisAPI.get_help(context)	×
22
23
24	@raw_data.command("store")	1✔
25	@DRY_RUN	1✔
26	@ARGUMENT_CASE_ID	1✔
27	@click.pass_context	1✔
28	def store_raw_data_analysis(context: click.Context, case_id: str, dry_run: bool = False):	1✔
29	LOG.info(f"Creating an analysis for case {case_id}")	1✔
30
31	if dry_run:	1✔
32	return	×
33
34	raw_data_service = RawDataAnalysisService(	1✔
35	store=context.obj.status_db,
36	trailblazer_api=context.obj.trailblazer_api,
37	)
38	raw_data_service.store_analysis(case_id)	1✔
39
40
41	@raw_data.command("store-available")	1✔
42	@DRY_RUN	1✔
43	@click.pass_context	1✔
44	def store_available_raw_data_analysis(context: click.Context, dry_run: bool = False):	1✔
45	"""Creates an analysis object in status-db for all raw data cases to be delivered."""
46	status_db: Store = context.obj.status_db	×
NEW 47	was_successful: bool = True	×
48	for case in status_db.get_cases_to_analyze(workflow=Workflow.RAW_DATA):	×
49	LOG.info(f"Creating an analysis for case {case.internal_id}")	×
50	if SequencingQCService.case_pass_sequencing_qc(case):	×
51	if dry_run:	×
52	return	×
NEW 53	try:	×
NEW 54	raw_data_service = RawDataAnalysisService(	×
55	store=context.obj.status_db,
56	trailblazer_api=context.obj.trailblazer_api,
57	)
NEW 58	raw_data_service.store_analysis(case.internal_id)	×
NEW 59	except Exception as error:	×
NEW 60	LOG.error(f"Failed to store analysis for case {case.internal_id}: {error}")	×
NEW 61	was_successful = False	×
NEW 62	if not was_successful:	×
NEW 63	raise click.Abort()	×

Clinical-Genomics / cg / 15705278932

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