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

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53.33

/trailblazer/services/slurm/slurm_api_service/slurm_api_service.py

from trailblazer.clients.slurm_api_client.dto.job_response import SlurmJobResponse
from trailblazer.clients.slurm_api_client.slurm_api_client import SlurmAPIClient
from trailblazer.services.slurm.dtos import SlurmJobInfo
from trailblazer.services.slurm.slurm_api_service.mappers import create_job
from trailblazer.services.slurm.slurm_api_service.utils import create_job_info_dto
from trailblazer.services.slurm.slurm_service import SlurmService
from trailblazer.services.slurm.utils import get_slurm_job_ids
from trailblazer.store.models import Analysis, Job
from trailblazer.store.store import Store


class SlurmAPIService(SlurmService):
    def __init__(self, client: SlurmAPIClient, store: Store):
        self.client = client
        self.store = store

    def get_job(self, job_id: int) -> SlurmJobInfo:
        job_response: SlurmJobResponse = self.client.get_job(job_id)
        return create_job_info_dto(job_response)

    def update_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)

        dtos: list[SlurmJobInfo] = []
        for job_id in job_ids:
            if job := self.get_job(job_id):
                dtos.append(job)

        jobs: list[Job] = [create_job(dto) for dto in dtos]
        self.store.replace_jobs(analysis_id=analysis_id, jobs=jobs)

    def cancel_jobs(self, analysis_id: int) -> None:
        analysis: Analysis = self.store.get_analysis_with_id(analysis_id)
        jobs: list[Job] = analysis.jobs

        for job in jobs:
            self.client.cancel_job(job.slurm_id)

1	from trailblazer.clients.slurm_api_client.dto.job_response import SlurmJobResponse	1✔
2	from trailblazer.clients.slurm_api_client.slurm_api_client import SlurmAPIClient	1✔
3	from trailblazer.services.slurm.dtos import SlurmJobInfo	1✔
4	from trailblazer.services.slurm.slurm_api_service.mappers import create_job	1✔
5	from trailblazer.services.slurm.slurm_api_service.utils import create_job_info_dto	1✔
6	from trailblazer.services.slurm.slurm_service import SlurmService	1✔
7	from trailblazer.services.slurm.utils import get_slurm_job_ids	1✔
8	from trailblazer.store.models import Analysis, Job	1✔
9	from trailblazer.store.store import Store	1✔
10
11
12	class SlurmAPIService(SlurmService):	1✔
13	def __init__(self, client: SlurmAPIClient, store: Store):	1✔
14	self.client = client	1✔
15	self.store = store	1✔
16
17	def get_job(self, job_id: int) -> SlurmJobInfo:	1✔
18	job_response: SlurmJobResponse = self.client.get_job(job_id)	×
19	return create_job_info_dto(job_response)	×
20
21	def update_jobs(self, analysis_id: int) -> None:	1✔
NEW 22	analysis: Analysis = self.store.get_analysis_with_id(analysis_id)	×
NEW 23	job_ids: list[int] = get_slurm_job_ids(analysis.config_path)	×
24
NEW 25	dtos: list[SlurmJobInfo] = []	×
26	for job_id in job_ids:	×
NEW 27	if job := self.get_job(job_id):	×
NEW 28	dtos.append(job)	×
29
NEW 30	jobs: list[Job] = [create_job(dto) for dto in dtos]	×
NEW 31	self.store.replace_jobs(analysis_id=analysis_id, jobs=jobs)	×
32
33	def cancel_jobs(self, analysis_id: int) -> None:	1✔
NEW 34	analysis: Analysis = self.store.get_analysis_with_id(analysis_id)	×
NEW 35	jobs: list[Job] = analysis.jobs	×
36
NEW 37	for job in jobs:	×
NEW 38	self.client.cancel_job(job.slurm_id)	×

Clinical-Genomics / trailblazer / 10403778022

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