10403778022

Committed 15 Aug 2024 12:29PM UTC coverage: 86.292%. First build

Build # 10403778022

Build Type

Pull #463

github

Committed by

seallard

Commit Message

Add integration test

Pull Request Pull Request #463: Clean up tower and slurm interactions

Run Details

156 of 221 new or added lines in 20 files covered. (70.59%)

2027 of 2349 relevant lines covered (86.29%)

0.86 hits per line

Source File
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62.5

/trailblazer/services/slurm/slurm_cli_service/slurm_cli_service.py

from trailblazer.apps.slurm.models import SqueueJob, SqueueResult
from trailblazer.clients.slurm_cli_client.slurm_cli_client import SlurmCLIClient
from trailblazer.clients.slurm_cli_client.utils import create_job_info_dto
from trailblazer.services.slurm.dtos import SlurmJobInfo
from trailblazer.services.slurm.slurm_service import SlurmService
from trailblazer.services.slurm.utils import get_slurm_job_ids
from trailblazer.store.models import Analysis
from trailblazer.store.store import Store


class SlurmCLIService(SlurmService):
    def __init__(self, client: SlurmCLIClient, store: Store):
        self.client = client
        self.store = store

    def get_job(self, job_id: int) -> SlurmJobInfo:
        queue: SqueueResult = self.client.get_slurm_queue([job_id])
        job: SqueueJob = queue.jobs[0]
        return create_job_info_dto(job)

    def update_jobs(self, job_ids: list[int]) -> list[SlurmJobInfo]:
        queue: SqueueResult = self.client.get_slurm_queue(job_ids)
        return [create_job_info_dto(job) for job in queue.jobs]

    def cancel_jobs(self, analysis_id: int) -> None:
        analysis: Analysis = self.store.get_analysis_with_id(analysis_id)
        job_ids: list[int] = get_slurm_job_ids(analysis.config_path)
        for job_id in job_ids:
            self.client.cancel_job(job_id)

1	from trailblazer.apps.slurm.models import SqueueJob, SqueueResult	1✔
2	from trailblazer.clients.slurm_cli_client.slurm_cli_client import SlurmCLIClient	1✔
3	from trailblazer.clients.slurm_cli_client.utils import create_job_info_dto	1✔
4	from trailblazer.services.slurm.dtos import SlurmJobInfo	1✔
5	from trailblazer.services.slurm.slurm_service import SlurmService	1✔
6	from trailblazer.services.slurm.utils import get_slurm_job_ids	1✔
7	from trailblazer.store.models import Analysis	1✔
8	from trailblazer.store.store import Store	1✔
9
10
11	class SlurmCLIService(SlurmService):	1✔
12	def __init__(self, client: SlurmCLIClient, store: Store):	1✔
13	self.client = client	1✔
14	self.store = store	1✔
15
16	def get_job(self, job_id: int) -> SlurmJobInfo:	1✔
17	queue: SqueueResult = self.client.get_slurm_queue([job_id])	×
18	job: SqueueJob = queue.jobs[0]	×
19	return create_job_info_dto(job)	×
20
21	def update_jobs(self, job_ids: list[int]) -> list[SlurmJobInfo]:	1✔
22	queue: SqueueResult = self.client.get_slurm_queue(job_ids)	×
23	return [create_job_info_dto(job) for job in queue.jobs]	×
24
25	def cancel_jobs(self, analysis_id: int) -> None:	1✔
NEW 26	analysis: Analysis = self.store.get_analysis_with_id(analysis_id)	×
NEW 27	job_ids: list[int] = get_slurm_job_ids(analysis.config_path)	×
NEW 28	for job_id in job_ids:	×
NEW 29	self.client.cancel_job(job_id)	×

Clinical-Genomics / trailblazer / 10403778022

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