tcga-downloader/tests/test_manifest.py

from tcga_downloader.manifest import (
    ManifestRecord,
    format_manifest_stats,
    get_manifest_stats,
    load_manifest,
    validate_files_against_manifest,
    validate_manifest,
    write_manifest,
)


def test_manifest_roundtrip_tsv(tmp_path):
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="abc",
        )
    ]
    path = tmp_path / "m.tsv"
    write_manifest(records, path, fmt="tsv")
    loaded = load_manifest(path)

    expected = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Unknown",
            data_format="Unknown",
            size=123,
            md5="abc",
        )
    ]
    assert loaded == expected


def test_manifest_roundtrip_json(tmp_path):
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="abc",
        )
    ]
    path = tmp_path / "m.json"
    write_manifest(records, path, fmt="json")
    loaded = load_manifest(path)
    assert loaded == records


def test_get_manifest_stats():
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=1000,
            md5="abc",
        ),
        ManifestRecord(
            file_id="f2",
            file_name="b.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=2000,
            md5="def",
        ),
        ManifestRecord(
            file_id="f3",
            file_name="c.tsv",
            data_type="Copy Number",
            data_format="TSV",
            size=3000,
            md5="ghi",
        ),
    ]

    stats = get_manifest_stats(records)

    assert stats["file_count"] == 3
    assert stats["total_size_bytes"] == 6000
    assert stats["total_size_mb"] == 6000 / (1024 * 1024)
    assert stats["total_size_gb"] == 6000 / (1024 * 1024 * 1024)
    assert stats["data_types"] == {"Gene Expression": 2, "Copy Number": 1}
    assert stats["data_formats"] == {"TSV": 3}


def test_format_manifest_stats():
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=1000,
            md5="abc",
        ),
    ]

    stats = get_manifest_stats(records)
    formatted = format_manifest_stats(stats)

    assert "File count: 1" in formatted
    assert "Total size:" in formatted
    assert "Data types:" in formatted
    assert "Gene Expression: 1" in formatted
    assert "Data formats:" in formatted
    assert "TSV: 1" in formatted


def test_validate_manifest_valid():
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="a" * 32,
        )
    ]
    errors = validate_manifest(records)
    assert len(errors) == 0


def test_validate_manifest_missing_fields():
    records = [
        ManifestRecord(
            file_id="",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="a" * 32,
        ),
        ManifestRecord(
            file_id="f2",
            file_name="",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="a" * 32,
        ),
        ManifestRecord(
            file_id="f3", file_name="c.tsv", data_type="", data_format="TSV", size=123, md5="a" * 32
        ),
        ManifestRecord(
            file_id="f4",
            file_name="d.tsv",
            data_type="Gene Expression",
            data_format="",
            size=123,
            md5="a" * 32,
        ),
    ]
    errors = validate_manifest(records)
    assert len(errors) == 4


def test_validate_manifest_invalid_md5():
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="invalid",
        )
    ]
    errors = validate_manifest(records)
    assert len(errors) == 1
    assert "MD5" in errors[0]


def test_validate_manifest_invalid_size():
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="a.tsv",
            data_type="Gene Expression",
            data_format="TSV",
            size=-1,
            md5="a" * 32,
        )
    ]
    errors = validate_manifest(records)
    assert len(errors) == 1
    assert "size" in errors[0].lower()


def test_validate_files_against_manifest(tmp_path):
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="file1.txt",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="d41d8cd98f00b204e9800998ecf8427e",
        ),
    ]
    data_dir = tmp_path / "data"
    data_dir.mkdir()

    file1 = data_dir / "file1.txt"
    file1.write_text("Hello")

    missing, checksum_errors = validate_files_against_manifest(records, data_dir)
    assert len(missing) == 0
    assert len(checksum_errors) == 1
    assert "file1.txt" in checksum_errors[0]


def test_validate_files_missing(tmp_path):
    records = [
        ManifestRecord(
            file_id="f1",
            file_name="file1.txt",
            data_type="Gene Expression",
            data_format="TSV",
            size=123,
            md5="a" * 32,
        ),
    ]
    data_dir = tmp_path / "data"
    data_dir.mkdir()

    missing, checksum_errors = validate_files_against_manifest(records, data_dir)
    assert len(missing) == 1
    assert "file1.txt" in missing[0]
    assert len(checksum_errors) == 0