11324534123

Committed 14 Oct 2024 09:14AM UTC coverage: 83.091%. First build

Build # 11324534123

Build Type

Pull #3841

github

Committed by

web-flow

Commit Message

Merge 232ad2057 into 9f13f37f4

Pull Request Pull Request #3841: post process all runs calling service over a list of run names

Run Details

49 of 73 new or added lines in 7 files covered. (67.12%)

19130 of 23023 relevant lines covered (83.09%)

0.99 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_all_run_names, 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
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."""
    exit_success: bool = True
    run_names: list[str] = get_all_run_names(context=context)
    for run_name in run_names:
        try:
            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)
        except Exception as error:
            LOG.error(f"{error}")
            exit_success = False
    if not exit_success:
        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_all_run_names, 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	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	exit_success: bool = True	×
NEW 44	run_names: list[str] = get_all_run_names(context=context)	×
NEW 45	for run_name in run_names:	×
NEW 46	try:	×
NEW 47	post_processing_service: PostProcessingService = (	×
48	get_post_processing_service_from_run_name(context=context, run_name=run_name)
49	)
NEW 50	post_processing_service.post_process(run_name=run_name, dry_run=dry_run)	×
NEW 51	except Exception as error:	×
NEW 52	LOG.error(f"{error}")	×
NEW 53	exit_success = False	×
NEW 54	if not exit_success:	×
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 / 11324534123

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