11890272117

Committed 18 Nov 2024 10:14AM UTC coverage: 84.467%. First build

Build # 11890272117

Build Type

Pull #3926

github

Committed by

web-flow

Commit Message

Merge a7149a3a7 into 40c89d2a7

Pull Request Pull Request #3926: Refactor get cases for analysis

Run Details

13 of 14 new or added lines in 3 files covered. (92.86%)

23416 of 27722 relevant lines covered (84.47%)

0.84 hits per line

Source File
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72.97

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

import logging

import 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
    for case in status_db.get_cases_to_analyse(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
            raw_data_service = RawDataAnalysisService(
                store=context.obj.status_db,
                trailblazer_api=context.obj.trailblazer_api,
            )
            raw_data_service.store_analysis(case.internal_id)

1	import logging	1✔
2
3	import 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	for case in status_db.get_cases_to_analyse(workflow=Workflow.RAW_DATA):	×
48	LOG.info(f"Creating an analysis for case {case.internal_id}")	×
49	if SequencingQCService.case_pass_sequencing_qc(case):	×
50	if dry_run:	×
51	return	×
52	raw_data_service = RawDataAnalysisService(	×
53	store=context.obj.status_db,
54	trailblazer_api=context.obj.trailblazer_api,
55	)
56	raw_data_service.store_analysis(case.internal_id)	×

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