11294476725

Committed 11 Oct 2024 02:48PM UTC coverage: 83.512%. First build

Build # 11294476725

Build Type

Pull #3832

github

Committed by

web-flow

Commit Message

Merge 3043d180d into 560003d27

Pull Request Pull Request #3832: feat - new post process all command

Run Details

48 of 81 new or added lines in 7 files covered. (59.26%)

20295 of 24302 relevant lines covered (83.51%)

0.94 hits per line

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60.0

/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, RunDirectoryNamesServices
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
    names_services: RunDirectoryNamesServices = context.run_directory_names_services
    are_all_services_successful: bool = True
    for service, name_service in [(services.pacbio, names_services.pacbio)]:
        try:
            service.post_process_all(
                run_directory_names=name_service.get_run_names(), dry_run=dry_run
            )
        except Exception as error:
            LOG.error(f"{error}")
            are_all_services_successful = False
    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, RunDirectoryNamesServices	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	names_services: RunDirectoryNamesServices = context.run_directory_names_services	×
NEW 45	are_all_services_successful: bool = True	×
NEW 46	for service, name_service in [(services.pacbio, names_services.pacbio)]:	×
NEW 47	try:	×
NEW 48	service.post_process_all(	×
49	run_directory_names=name_service.get_run_names(), dry_run=dry_run
50	)
NEW 51	except Exception as error:	×
NEW 52	LOG.error(f"{error}")	×
NEW 53	are_all_services_successful = False	×
NEW 54	if not are_all_services_successful:	×
NEW 55	raise click.Abort	×
56
57
58	post_process_group.add_command(post_process_run)	1✔
59	post_process_group.add_command(post_process_all_runs)	1✔

Clinical-Genomics / cg / 11294476725

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