9460843507

Committed 11 Jun 2024 06:42AM UTC coverage: 84.664%. First build

Build # 9460843507

Build Type

Pull #3329

github

Committed by

web-flow

Commit Message

Merge 768870696 into fa05c0cfe

Pull Request Pull Request #3329: feature(downsample api parameters)

Run Details

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75.56

/cg/cli/downsample.py

"""cg module for downsampling reads in a sample."""

import logging
from pathlib import Path
from typing import Tuple

import click

from cg.apps.downsample.downsample import DownsampleAPI
from cg.apps.downsample.models import DownsampleInput
from cg.apps.downsample.utils import store_downsampled_sample_bundle
from cg.constants.constants import DRY_RUN
from cg.models.cg_config import CGConfig

LOG = logging.getLogger(__name__)


@click.group()
def downsample():
    """Downsample reads in a sample."""


@downsample.command(
    "samples",
    help="Downsample reads in one or multiple samples in a case. Usage: \n"
    "For a single sample: cg downsample samples -c supersonicturtle -cn new_case_name -i ACC1234 0.1\n"
    "For multiple samples:cg downsample samples -c supersonicturtle -cn new_case_name -i ACC1234 0.1 -i ACC12324 10",
)
@click.option(
    "-c",
    "--case-id",
    required=True,
    help="Case identifier used in statusdb, e.g. supersonicturtle. The case information wil be transferred to the downsampled case.",
)
@click.option(
    "-cn",
    "--case-name",
    required=True,
    help="Case name that is used as name for the downsampled case.",
)
@click.option(
    "-a",
    "--account",
    required=False,
    default=None,
    help="Please specify the account to use for the downsampling. Defaults to production (production) or development (stage) account if not specified.",
)
@click.option(
    "-i",
    "--input-data",
    required=True,
    nargs=2,
    multiple=True,
    help="Identifier used in statusdb, e.g. ACC1234567 and the number of reads to down sample to in millions separated by a space"
    " e.g. ACC1234567 30.0. Multiple inputs can be provided.",
)
@click.option(
    "--action",
    required=False,
    default=None,
    help="Set the action of the case in statusDB, e.g. HOLD. Default is to keep the action from the original case.",
)
@click.option(
    "--ticket",
    required=False,
    default=None,
    help="Set the ticket number for the case in statusDB. Default is to keep the ticket number from the original case.",
)
@click.option(
    "--customer-id",
    required=False,
    default=None,
    help="Set the customer for the case in statusDB, e.g. cust000. Default is to keep the customer from the original case.",
)
@click.option(
    "--data-analysis",
    required=False,
    default=None,
    help="Set the data analysis for the case in statusDB, e.g. MIP_DNA. Default is to keep the data analysis from the original case.",
)
@click.option(
    "--data-delivery",
    required=False,
    default=None,
    help="Set the data delivery for the case in statusDB, e.g. fastq. Default is to keep the data delivery from the original case.",
)
@DRY_RUN
@click.pass_obj
def downsample_sample(
    context: CGConfig,
    case_id: str,
    case_name: str,
    account: str | None,
    input_data: Tuple[str, float],
    action: str | None,
    ticket: str | None,
    customer_id: str | None,
    data_analysis: str | None,
    data_delivery: str | None,
    dry_run: bool,
):
    """Downsample reads in one or multiple samples."""
    downsample_api = DownsampleAPI(config=context, dry_run=dry_run)
    for sample_id, reads in input_data:
        downsample_input = DownsampleInput(
            case_id=case_id,
            sample_id=sample_id,
            number_of_reads=float(reads),
            case_name=case_name,
            account=account,
            action=action,
            ticket=ticket,
            customer_id=customer_id,
            data_analysis=data_analysis,
            data_delivery=data_delivery,
        )
        try:
            downsample_api.downsample_sample(downsample_input=downsample_input)
        except Exception as error:
            LOG.info(repr(error))
            continue


@downsample.command(
    "store",
    help="Store the downsampled fastq files in housekeeper.\n "
    "Make sure the downsample sbtach job has finished before using this command! \n"
    "Usage: cg downsample store ACC123145DS2C0M ACC1231DS30C0M",
)
@click.argument("sample_ids", type=str, nargs=-1)
@click.pass_obj
def store_downsampled_samples(context: CGConfig, sample_ids: list[str]):
    """Store fastq files for downsampled samples in Housekeeper."""
    for sample_id in sample_ids:
        downsample_dir: str = str(Path(context.downsample.downsample_dir, sample_id))
        LOG.debug(f"Searching for fastq files in : {downsample_dir}")
        try:
            store_downsampled_sample_bundle(
                housekeeper_api=context.housekeeper_api,
                sample_id=sample_id,
                fastq_file_output_directory=downsample_dir,
            )
        except Exception as error:
            LOG.info(repr(error))
            continue

1	"""cg module for downsampling reads in a sample."""
2
3	import logging	1✔
4	from pathlib import Path	1✔
5	from typing import Tuple	1✔
6
7	import click	1✔
8
9	from cg.apps.downsample.downsample import DownsampleAPI	1✔
10	from cg.apps.downsample.models import DownsampleInput	1✔
11	from cg.apps.downsample.utils import store_downsampled_sample_bundle	1✔
12	from cg.constants.constants import DRY_RUN	1✔
13	from cg.models.cg_config import CGConfig	1✔
14
15	LOG = logging.getLogger(__name__)	1✔
16
17
18	@click.group()	1✔
19	def downsample():	1✔
20	"""Downsample reads in a sample."""
21
22
23	@downsample.command(	1✔
24	"samples",
25	help="Downsample reads in one or multiple samples in a case. Usage: \n"
26	"For a single sample: cg downsample samples -c supersonicturtle -cn new_case_name -i ACC1234 0.1\n"
27	"For multiple samples:cg downsample samples -c supersonicturtle -cn new_case_name -i ACC1234 0.1 -i ACC12324 10",
28	)
29	@click.option(	1✔
30	"-c",
31	"--case-id",
32	required=True,
33	help="Case identifier used in statusdb, e.g. supersonicturtle. The case information wil be transferred to the downsampled case.",
34	)
35	@click.option(	1✔
36	"-cn",
37	"--case-name",
38	required=True,
39	help="Case name that is used as name for the downsampled case.",
40	)
41	@click.option(	1✔
42	"-a",
43	"--account",
44	required=False,
45	default=None,
46	help="Please specify the account to use for the downsampling. Defaults to production (production) or development (stage) account if not specified.",
47	)
48	@click.option(	1✔
49	"-i",
50	"--input-data",
51	required=True,
52	nargs=2,
53	multiple=True,
54	help="Identifier used in statusdb, e.g. ACC1234567 and the number of reads to down sample to in millions separated by a space"
55	" e.g. ACC1234567 30.0. Multiple inputs can be provided.",
56	)
57	@click.option(	1✔
58	"--action",
59	required=False,
60	default=None,
61	help="Set the action of the case in statusDB, e.g. HOLD. Default is to keep the action from the original case.",
62	)
63	@click.option(	1✔
64	"--ticket",
65	required=False,
66	default=None,
67	help="Set the ticket number for the case in statusDB. Default is to keep the ticket number from the original case.",
68	)
69	@click.option(	1✔
70	"--customer-id",
71	required=False,
72	default=None,
73	help="Set the customer for the case in statusDB, e.g. cust000. Default is to keep the customer from the original case.",
74	)
75	@click.option(	1✔
76	"--data-analysis",
77	required=False,
78	default=None,
79	help="Set the data analysis for the case in statusDB, e.g. MIP_DNA. Default is to keep the data analysis from the original case.",
80	)
81	@click.option(	1✔
82	"--data-delivery",
83	required=False,
84	default=None,
85	help="Set the data delivery for the case in statusDB, e.g. fastq. Default is to keep the data delivery from the original case.",
86	)
87	@DRY_RUN	1✔
88	@click.pass_obj	1✔
89	def downsample_sample(	1✔
90	context: CGConfig,
91	case_id: str,
92	case_name: str,
93	account: str \| None,
94	input_data: Tuple[str, float],
95	action: str \| None,
96	ticket: str \| None,
97	customer_id: str \| None,
98	data_analysis: str \| None,
99	data_delivery: str \| None,
100	dry_run: bool,
101	):
102	"""Downsample reads in one or multiple samples."""
103	downsample_api = DownsampleAPI(config=context, dry_run=dry_run)	×
104	for sample_id, reads in input_data:	×
NEW 105	downsample_input = DownsampleInput(	×
106	case_id=case_id,
107	sample_id=sample_id,
108	number_of_reads=float(reads),
109	case_name=case_name,
110	account=account,
111	action=action,
112	ticket=ticket,
113	customer_id=customer_id,
114	data_analysis=data_analysis,
115	data_delivery=data_delivery,
116	)
117	try:	×
NEW 118	downsample_api.downsample_sample(downsample_input=downsample_input)	×
119	except Exception as error:	×
120	LOG.info(repr(error))	×
121	continue	×
122
123
124	@downsample.command(	1✔
125	"store",
126	help="Store the downsampled fastq files in housekeeper.\n "
127	"Make sure the downsample sbtach job has finished before using this command! \n"
128	"Usage: cg downsample store ACC123145DS2C0M ACC1231DS30C0M",
129	)
130	@click.argument("sample_ids", type=str, nargs=-1)	1✔
131	@click.pass_obj	1✔
132	def store_downsampled_samples(context: CGConfig, sample_ids: list[str]):	1✔
133	"""Store fastq files for downsampled samples in Housekeeper."""
134	for sample_id in sample_ids:	1✔
135	downsample_dir: str = str(Path(context.downsample.downsample_dir, sample_id))	1✔
136	LOG.debug(f"Searching for fastq files in : {downsample_dir}")	1✔
137	try:	1✔
138	store_downsampled_sample_bundle(	1✔
139	housekeeper_api=context.housekeeper_api,
140	sample_id=sample_id,
141	fastq_file_output_directory=downsample_dir,
142	)
143	except Exception as error:	×
144	LOG.info(repr(error))	×
145	continue	×

Clinical-Genomics / cg / 9460843507

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