feat: add gdc-client downloader

tcga_downloader/download.py

@@ -0,0 +1,28 @@
+from __future__ import annotations
+
+import shutil
+import subprocess
+from pathlib import Path
+
+
+def build_gdc_command(manifest_path: Path, out_dir: Path, processes: int, retries: int) -> list[str]:
+    return [
+        "gdc-client",
+        "download",
+        "-m",
+        str(manifest_path),
+        "-d",
+        str(out_dir),
+        "--n-processes",
+        str(processes),
+        "--retry-count",
+        str(retries),
+        "--checksum",
+    ]
+
+
+def run_gdc_download(manifest_path: Path, out_dir: Path, processes: int = 4, retries: int = 3) -> None:
+    if not shutil.which("gdc-client"):
+        raise RuntimeError("gdc-client not found in PATH")
+    cmd = build_gdc_command(manifest_path, out_dir, processes, retries)
+    subprocess.run(cmd, check=True)

tests/test_download.py

@@ -0,0 +1,9 @@
+from pathlib import Path
+
+from tcga_downloader.download import build_gdc_command
+
+
+def test_build_gdc_command():
+    cmd = build_gdc_command(Path("/tmp/m.tsv"), Path("/data"), processes=4, retries=3)
+    assert "gdc-client" in cmd[0]
+    assert "-m" in cmd