def METHOD_NAME(self):
    base = Path("ml_ready")
    inputs = base / "input"
    with self.preparation_stage():
        collection, sample_1 = self.prepare_collection_with_one_sample()
        self.prepare_exp_matrix(
            sample_ids=[sample_1.id],
            feature_ids=["ENSG00000178591", "ENSG00000101255"],
            outfile=str(TEST_FILES_DIR / inputs / "exp_matrix.tsv"),
        )
        ref_space = self.run_process(
            "reference-space",
            {
                "name": "My name",
                "description": "My description",
                "source": "ENSEMBL",
                "species": "Homo sapiens",
                "training_data": str(inputs / "exp_matrix.tsv"),
                "preprocessor": str(inputs / "preprocessor.pickle"),
            },
            collection=collection,
        )
    ml_exp = self.run_process(
        "upload-ml-expression",
        {
            "source": "ENSEMBL",
            "species": "Homo sapiens",
            "exp": str(inputs / "exp_matrix.tsv"),
            "reference_space": ref_space.id,
        },
        collection=collection,
    )
    self.assertEqual(ml_exp.output["source"], "ENSEMBL")
    self.assertEqual(ml_exp.output["species"], "Homo sapiens")
    # Cannot test with assertFile, like:
    # self.assertFile(ml_exp, "exp", outputs / "exp_matrix.tsv")
    # Since it is not possible to predict sample ID during tests
    # Get the original data
    with open(str(TEST_FILES_DIR / inputs / "exp_matrix.tsv")) as handle:
        contents_original = [line.strip().split("\t") for line in handle]
    # Get the processed data
    exp_path = ml_exp.location.get_path(filename=ml_exp.output["exp"]["file"])
    with open(exp_path) as handle:
        contents_test = [line.strip().split("\t") for line in handle]
    self.assertTrue(len(contents_test) == len(contents_original) == 2)
    # Header needs to start with sample_id and than sorted features
    self.assertEqual(
        contents_test[0],
        [contents_original[0][0]] + sorted(contents_original[0][1:]),
    )
    # Only one line, test except for sample id
    self.assertCountEqual(contents_test[1][1:], contents_original[1][1:])