10158976052

Committed 30 Jul 2024 08:34AM UTC coverage: 83.666%. First build

Build # 10158976052

Build Type

Pull #3485

github

Committed by

web-flow

Commit Message

Merge 950693aae into 8380cf2de

Pull Request Pull Request #3485: Add cli post processing

Run Details

17 of 57 new or added lines in 5 files covered. (29.82%)

19464 of 23264 relevant lines covered (83.67%)

0.91 hits per line

Source File
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53.33

/cg/services/post_processing/pacbio/post_processing_service.py

from cg.services.post_processing.abstract_classes import PostProcessingService
from cg.services.post_processing.pacbio.data_storage_service.pacbio_store_service import (
    PacBioStoreService,
)
from cg.services.post_processing.pacbio.housekeeper_service.pacbio_houskeeper_service import (
    PacBioHousekeeperService,
)
from cg.services.post_processing.pacbio.run_data_generator.pacbio_run_data_generator import (
    PacBioRunDataGenerator,
)
from cg.services.post_processing.pacbio.run_data_generator.run_data import PacBioRunData


class PacBioPostProcessingService(PostProcessingService):
    """Service for handling post-processing of PacBio sequencing runs."""

    def __init__(
        self,
        run_data_generator: PacBioRunDataGenerator,
        hk_service: PacBioHousekeeperService,
        store_service: PacBioStoreService,
        sequencing_dir: str,
    ):
        self.run_data_generator: PacBioRunDataGenerator = run_data_generator
        self.hk_service: PacBioHousekeeperService = hk_service
        self.store_service: PacBioStoreService = store_service
        self.sequencing_dir: str = sequencing_dir

    def post_process(self, run_name: str):
        run_data: PacBioRunData = self.run_data_generator.get_run_data(
            run_name=run_name, sequencing_dir=self.sequencing_dir
        )
        self.store_service.store_post_processing_data(run_data=run_data)
        self.hk_service.store_files_in_housekeeper(run_data=run_data)

1	from cg.services.post_processing.abstract_classes import PostProcessingService	1✔
2	from cg.services.post_processing.pacbio.data_storage_service.pacbio_store_service import (	1✔
3	PacBioStoreService,
4	)
5	from cg.services.post_processing.pacbio.housekeeper_service.pacbio_houskeeper_service import (	1✔
6	PacBioHousekeeperService,
7	)
8	from cg.services.post_processing.pacbio.run_data_generator.pacbio_run_data_generator import (	1✔
9	PacBioRunDataGenerator,
10	)
11	from cg.services.post_processing.pacbio.run_data_generator.run_data import PacBioRunData	1✔
12
13
14	class PacBioPostProcessingService(PostProcessingService):	1✔
15	"""Service for handling post-processing of PacBio sequencing runs."""
16
17	def __init__(	1✔
18	self,
19	run_data_generator: PacBioRunDataGenerator,
20	hk_service: PacBioHousekeeperService,
21	store_service: PacBioStoreService,
22	sequencing_dir: str,
23	):
24	self.run_data_generator: PacBioRunDataGenerator = run_data_generator	×
25	self.hk_service: PacBioHousekeeperService = hk_service	×
26	self.store_service: PacBioStoreService = store_service	×
NEW 27	self.sequencing_dir: str = sequencing_dir	×
28
29	def post_process(self, run_name: str):	1✔
30	run_data: PacBioRunData = self.run_data_generator.get_run_data(	×
31	run_name=run_name, sequencing_dir=self.sequencing_dir
32	)
33	self.store_service.store_post_processing_data(run_data=run_data)	×
34	self.hk_service.store_files_in_housekeeper(run_data=run_data)	×

Clinical-Genomics / cg / 10158976052

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