11237273489

Committed 08 Oct 2024 02:09PM UTC coverage: 84.465%. First build

Build # 11237273489

Build Type

Pull #3818

github

Committed by

web-flow

Commit Message

Merge 25d0d263a into 94fa764b0

Pull Request Pull Request #3818: add cli command post process all

Run Details

35 of 53 new or added lines in 5 files covered. (66.04%)

22880 of 27088 relevant lines covered (84.47%)

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67.74

/cg/cli/post_process/post_process.py

"""CLI commands to post-process a sequencing run."""

import logging

import click

from cg.cli.post_process.utils import get_post_processing_service_from_run_name
from cg.cli.utils import CLICK_CONTEXT_SETTINGS
from cg.constants.cli_options import DRY_RUN
from cg.models.cg_config import CGConfig, PostProcessingServices
from cg.services.run_devices.abstract_classes import PostProcessingService

LOG = logging.getLogger(__name__)


@click.group(name="post-process", context_settings=CLICK_CONTEXT_SETTINGS)
def post_process_group():
    """Post-process sequencing runs from the sequencing instruments."""
    LOG.info("Running cg post-processing.")


@post_process_group.command(name="run")
@DRY_RUN
@click.argument("run-name")
@click.pass_obj
def post_process_run(context: CGConfig, run_name: str, dry_run: bool) -> None:
    """Post-process a sequencing run from the PacBio instrument.

    run-name is the full name of the sequencing unit of run. For example:
        PacBio: 'r84202_20240522_133539/1_A01'
    """
    post_processing_service: PostProcessingService = get_post_processing_service_from_run_name(
        context=context, run_name=run_name
    )
    post_processing_service.post_process(run_name=run_name, dry_run=dry_run)


@post_process_group.command(name="all")
@DRY_RUN
@click.pass_obj
def post_process_all_runs(context: CGConfig, dry_run: bool) -> None:
    """Post-process all runs from the instruments."""
    services: PostProcessingServices = context.post_processing_services
    are_all_services_successful: bool = True
    for service in [services.pacbio]:
        is_service_successful: bool = service.post_process_all(dry_run=dry_run)
        are_all_services_successful = are_all_services_successful and is_service_successful
    if not are_all_services_successful:
        raise click.Abort


post_process_group.add_command(post_process_run)
post_process_group.add_command(post_process_all_runs)

1	"""CLI commands to post-process a sequencing run."""
2
3	import logging	1✔
4
5	import click	1✔
6
7	from cg.cli.post_process.utils import get_post_processing_service_from_run_name	1✔
8	from cg.cli.utils import CLICK_CONTEXT_SETTINGS	1✔
9	from cg.constants.cli_options import DRY_RUN	1✔
10	from cg.models.cg_config import CGConfig, PostProcessingServices	1✔
11	from cg.services.run_devices.abstract_classes import PostProcessingService	1✔
12
13	LOG = logging.getLogger(__name__)	1✔
14
15
16	@click.group(name="post-process", context_settings=CLICK_CONTEXT_SETTINGS)	1✔
17	def post_process_group():	1✔
18	"""Post-process sequencing runs from the sequencing instruments."""
19	LOG.info("Running cg post-processing.")	×
20
21
22	@post_process_group.command(name="run")	1✔
23	@DRY_RUN	1✔
24	@click.argument("run-name")	1✔
25	@click.pass_obj	1✔
26	def post_process_run(context: CGConfig, run_name: str, dry_run: bool) -> None:	1✔
27	"""Post-process a sequencing run from the PacBio instrument.
28
29	run-name is the full name of the sequencing unit of run. For example:
30	PacBio: 'r84202_20240522_133539/1_A01'
31	"""
32	post_processing_service: PostProcessingService = get_post_processing_service_from_run_name(	×
33	context=context, run_name=run_name
34	)
35	post_processing_service.post_process(run_name=run_name, dry_run=dry_run)	×
36
37
38	@post_process_group.command(name="all")	1✔
39	@DRY_RUN	1✔
40	@click.pass_obj	1✔
41	def post_process_all_runs(context: CGConfig, dry_run: bool) -> None:	1✔
42	"""Post-process all runs from the instruments."""
NEW 43	services: PostProcessingServices = context.post_processing_services	×
NEW 44	are_all_services_successful: bool = True	×
NEW 45	for service in [services.pacbio]:	×
NEW 46	is_service_successful: bool = service.post_process_all(dry_run=dry_run)	×
NEW 47	are_all_services_successful = are_all_services_successful and is_service_successful	×
NEW 48	if not are_all_services_successful:	×
NEW 49	raise click.Abort	×
50
51
52	post_process_group.add_command(post_process_run)	1✔
53	post_process_group.add_command(post_process_all_runs)	1✔

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