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mecfs_bio.build_system.wf.base_wf

Classes:

  • WF –

    An interface to the external world.

Functions:

  • make_wf –

    Construct a WF, defaulting any capability not explicitly supplied.

WF

An interface to the external world.

To add a new capability, add an attribute here and a corresponding parameter to make_wf with an appropriate default.

Methods:

Attributes:

downloader instance-attribute 

downloader: WFDownloader

synapse_downloader instance-attribute 

synapse_downloader: SynapseDownloader

download_from_synapse 

download_from_synapse(
    synid: str, dest_dir: Path, expected_name: str
) -> Path

Download the single file at synid into dest_dir and return its path.

Source code in mecfs_bio/build_system/wf/base_wf.py 
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def download_from_synapse(
    self, synid: str, dest_dir: Path, expected_name: str
) -> Path:
    """Download the single file at synid into dest_dir and return its path."""
    return self.synapse_downloader.download(synid, dest_dir, expected_name)

download_from_url 

download_from_url(
    url: str, local_path: Path, md5_hash: str | None
) -> None
Source code in mecfs_bio/build_system/wf/base_wf.py 
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def download_from_url(
    self, url: str, local_path: Path, md5_hash: str | None
) -> None:
    self.downloader.download(url, local_path, md5_hash)

fetch_synapse_file_head 

fetch_synapse_file_head(synid: str, n_bytes: int) -> bytes

Return the first n_bytes of the Synapse file at synid without downloading the whole file (via a pre-signed URL + HTTP Range request).

Source code in mecfs_bio/build_system/wf/base_wf.py 
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def fetch_synapse_file_head(self, synid: str, n_bytes: int) -> bytes:
    """Return the first n_bytes of the Synapse file at synid without downloading the
    whole file (via a pre-signed URL + HTTP Range request)."""
    return self.synapse_downloader.fetch_file_head(synid, n_bytes)

make_wf 

make_wf(
    downloader: WFDownloader | None = None,
    synapse_downloader: SynapseDownloader | None = None,
) -> WF

Construct a WF, defaulting any capability not explicitly supplied.

Source code in mecfs_bio/build_system/wf/base_wf.py 
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def make_wf(
    downloader: WFDownloader | None = None,
    synapse_downloader: SynapseDownloader | None = None,
) -> WF:
    """Construct a WF, defaulting any capability not explicitly supplied."""
    return WF(
        downloader=downloader if downloader is not None else SimpleWFDownloader(),
        synapse_downloader=(
            synapse_downloader
            if synapse_downloader is not None
            else SharedClientSynapseDownloader()
        ),
    )