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DataLad FUSE extension package

codecov.io tests docs

datalad-fuse provides commands for reading files in a DataLad dataset from their remote web URLs without having to download them in their entirety first. Instead, fsspec is used to sparsely download and locally cache the files as needed.

Installation

Current version of datalad-fuse requires Python 3.7 or higher. Just use pip for Python 3 (You have pip, right?) to install it:

python3 -m pip install datalad-fuse

In addition, use of the datalad fusefs command requires FUSE to be installed; on Debian-based systems, this can be done with:

sudo apt-get install fuse

Commands

datalad fsspec-cache-clear [<options>]

Clears the local download cache for a dataset.

Options

  • -d <DATASET>, --dataset <DATASET> — Specify the dataset to operate on. If no dataset is given, an attempt is made to identify the dataset based on the current working directory.

  • -r, --recursive — Clear the caches of subdatasets as well.

datalad fsspec-head [<options>] <path>

Shows leading lines/bytes of an annexed file by fetching its data from a remote URL.

Options

  • -d <DATASET>, --dataset <DATASET> — Specify the dataset to operate on. If no dataset is given, an attempt is made to identify the dataset based on the current working directory.

  • -n <INT>, --lines <INT> — How many lines to show (default: 10)

  • -c <INT>, --bytes <INT> — How many bytes to show

datalad fusefs [<options>] <mount-path>

Create a read-only FUSE mount at <mount-path> that exposes the files in the given dataset. Opening a file under the mount that is not locally present in the dataset will cause its contents to be downloaded from the file's web URL as needed.

When the command finishes, fsspec-cache-clear may be run depending on the value of the datalad.fusefs.cache-clear configuration option. If it is set to "visited", then any (sub)datasets that were accessed in the FUSE mount will have their caches cleared; if it is instead set to "recursive", then all (sub)datasets in the dataset being operated on will have their caches cleared.

Options

  • --allow-other — Allow all users to access files in the mount. This requires setting user_allow_other in /etc/fuse.conf.

  • -d <DATASET>, --dataset <DATASET> — Specify the dataset to operate on. If no dataset is given, an attempt is made to identify the dataset based on the current working directory.

  • -f, --foreground — Run the FUSE process in the foreground; use Ctrl-C to exit. This option is currently required.

  • --mode-transparent — Expose the dataset's .git directory in the mount