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mecfs_bio.build_system.task.osf_retrieve_task

A task that fetches GWAS data from the Open Science data store

Classes:

  • OSFRetrievalTask –

    A task that fetches GWAS data from the Open Science data store

OSFRetrievalTask

Bases: GeneratingTask

A task that fetches GWAS data from the Open Science data store

Methods:

Attributes:

deps property 

deps: list[Task]

md5_hash class-attribute instance-attribute 

md5_hash: str | None = None

meta instance-attribute 

meta: GWASSummaryDataFileMeta

osf_project_id instance-attribute 

osf_project_id: str

run_command class-attribute instance-attribute 

run_command: Callable[[list[str]], str] = (
    execute_command_with_retries
)

execute 

execute(
    scratch_dir: Path, fetch: Fetch, wf: WF
) -> FileAsset
Source code in mecfs_bio/build_system/task/osf_retrieve_task.py 
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def execute(self, scratch_dir: Path, fetch: Fetch, wf: WF) -> FileAsset:
    tmp_dst = scratch_dir / "tmp"
    self.run_command(
        [
            "pixi",
            "r",
            "osf",
            "-p",
            self.osf_project_id,
            "fetch",
            "--force",
            shlex.quote(str(self.meta.project_path)),
            shlex.quote(str(tmp_dst)),
        ]
    )
    verify_hash(tmp_dst, self.md5_hash)

    return FileAsset(
        tmp_dst,
    )