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mecfs_bio.build_system.task.get_file_from_synapse_task

Task to get a file from synapse.org, a scientific data repository.

Classes:

  • GetFileFromSynapseTask –

    Task to get a file from synapse.org (see: https://docs.synapse.org/synapse-docs/faq)

Attributes:

logger module-attribute 

logger = structlog.getLogger()

GetFileFromSynapseTask

Bases: Task

Task to get a file from synapse.org (see: https://docs.synapse.org/synapse-docs/faq) May require authentication. See Getting Started.

Methods:

Attributes:

deps property 

deps: list[Task]

expected_filename instance-attribute 

expected_filename: str

meta instance-attribute 

meta: Meta

synid instance-attribute 

synid: str

execute 

execute(scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset
Source code in mecfs_bio/build_system/task/get_file_from_synapse_task.py 
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def execute(self, scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset:
    path = wf.download_from_synapse(self.synid, scratch_dir, self.expected_filename)
    logger.debug(f"downloaded: {path}")
    return FileAsset(path)