Legacy Client
=============

.. version-deprecated:: 0.3.7
   The legacy client is being phased out. Use :class:`flowbio.v2.Client` instead.

Example Usage
-------------

::

    import flowbio

    client = flowbio.Client()
    client.login("your_username", "your_password")

    # Upload standard data
    data = client.upload_data("/path/to/file.fa", progress=True, retries=5)
    print(data)

    # Upload sample
    sample = client.upload_sample(
        "My Sample Name",
        "/path/to/reads1.fastq.gz",
        "/path/to/reads2.fastq.gz",  # optional
        progress=True,
        metadata={
            "sample_type": "RNA-Seq",
            "scientist": "Charles Darwin",
            "strandedness": "reverse",
        }
    )
    print(sample)

    # Upload multiplexed
    multiplexed = client.upload_multiplexed(
        "/path/to/reads.fastq.gz",
        progress=True,
        retries=5,
    )
    print(multiplexed)

    # Upload annotation
    annotation = client.upload_annotation(
        "/path/to/annotation.csv",
        progress=True,
        retries=5,
    )
    print(annotation)

    # Run pipeline
    execution = client.run_pipeline(
        "RNA-Seq",
        "3.8.1",
        "23.04.3",
        params={"param1": "param2"},
        data_params={"fasta": 123456789},
    )

.. autoclass:: flowbio.Client
   :members: login, data, upload_data, upload_sample, upload_annotation, upload_multiplexed, sample, run_pipeline, execution, execute, refresh_token, user