from unittest.mock import patch

from tcga_downloader.cli import main


@patch(
    "sys.argv",
    [
        "tcga-downloader",
        "query",
        "--project",
        "TCGA-BRCA",
        "--data-type",
        "Gene Expression",
        "--out",
        "/tmp/m.tsv",
    ],
)
@patch("tcga_downloader.cli.query_files")
def test_cli_integration_query_full(mock_query, tmp_path, monkeypatch):
    mock_query.return_value = [
        {
            "file_id": "f1",
            "file_name": "file1.tsv",
            "data_type": "Gene Expression",
            "data_format": "TSV",
            "file_size": 1000,
            "md5sum": "a" * 32,
        }
    ]

    out_path = tmp_path / "m.tsv"
    monkeypatch.setattr(
        "sys.argv",
        [
            "tcga-downloader",
            "query",
            "--project",
            "TCGA-BRCA",
            "--data-type",
            "Gene Expression",
            "--out",
            str(out_path),
        ],
    )

    main()

    assert out_path.exists()
    assert mock_query.called


@patch("tcga_downloader.cli.run_gdc_download")
def test_cli_integration_download_with_manifest(mock_download, tmp_path):
    manifest_path = tmp_path / "manifest.tsv"
    manifest_path.write_text("file_id\tfile_name\t...\n")

    mock_download.return_value = None

    from unittest.mock import patch as patch2
    from tcga_downloader.cli import main

    with patch2(
        "sys.argv",
        [
            "tcga-downloader",
            "download",
            "--manifest",
            str(manifest_path),
            "--out-dir",
            str(tmp_path / "data"),
        ],
    ):
        main()

    assert mock_download.called


def test_cli_config_init_command(tmp_path):
    config_path = tmp_path / "config.json"

    from unittest.mock import patch
    from tcga_downloader.cli import main
    from tcga_downloader.config import load_config

    with patch("sys.argv", ["tcga-downloader", "config", "--init", str(config_path)]):
        main()

    assert config_path.exists()

    config = load_config(config_path)
    assert config.query.project == "TCGA-BRCA"
    assert config.query.data_type == "Gene Expression"