.. _`bio/ega/fetch`:

EGA FETCH
=========


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/ega/fetch?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/ega/fetch

Fetch files from EGA with pyega3.

**URL**: https://github.com/EGA-archive/ega-download-client

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule download_file:
        output:
            "data/{egafile}.cram",
        log:
            "logs/ega/fetch/{egafile}.log",
        params:
            fileid=lambda wildcards: wildcards.egafile,
            extra_pyega3="-t", # optional extra args for pyega3
            extra_fetch="",  # optional extra args for the fetch subcommand
        wrapper:
            "v3.3.3/bio/ega/fetch"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``pyega3=5.1.0``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    from pathlib import Path
    import shlex
    import shutil
    import subprocess as sp
    import sys
    import tempfile

    if snakemake.log:
        sys.stderr = open(snakemake.log[0], "w")

    fileid = snakemake.params.fileid

    fmt = Path(snakemake.output[0]).suffix[1:].upper()

    extra_pyega3 = shlex.split(snakemake.params.get("extra_pyega3", ""))
    extra_fetch = shlex.split(snakemake.params.get("extra_fetch", ""))

    with tempfile.TemporaryDirectory() as tmpdir:
        cmd = (
            ["pyega3"]
            + extra_pyega3
            + ["fetch", "--output-dir", tmpdir, "--format", fmt, fileid]
            + extra_fetch
        )
        sp.run(
            cmd,
            stdout=sys.stderr,
            stderr=sp.STDOUT,
            check=True,
        )
        # obtain path to the downloaded file (it should be the only file with that
        # extension in the temp dir)
        glob_res = list((Path(tmpdir) / fileid).glob(f"*.{fmt.lower()}"))
        assert (
            len(glob_res) == 1
        ), "bug: more than one file with desired extension downloaded by pyega3"

        # Move the file to the output
        shutil.move(glob_res[0], snakemake.output[0])


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