From 60e852de843a11546fc11ed5c4262ab7bc27fbe5 Mon Sep 17 00:00:00 2001
From: "yunpeng.zhang" <yunpeng.zhang@brbiotech.com>
Date: Fri, 16 Jan 2026 14:51:39 +0800
Subject: [PATCH] feat: add CLI entry points

---
 tcga_downloader/cli.py | 66 ++++++++++++++++++++++++++++++++++++++++++
 tests/test_cli.py      |  7 +++++
 2 files changed, 73 insertions(+)
 create mode 100644 tcga_downloader/cli.py
 create mode 100644 tests/test_cli.py

diff --git a/tcga_downloader/cli.py b/tcga_downloader/cli.py
new file mode 100644
index 0000000..5760155
--- /dev/null
+++ b/tcga_downloader/cli.py
@@ -0,0 +1,66 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+from tcga_downloader.download import run_gdc_download
+from tcga_downloader.manifest import ManifestRecord, write_manifest
+from tcga_downloader.query import query_files
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(prog="tcga-downloader")
+    sub = parser.add_subparsers(dest="command", required=True)
+
+    q = sub.add_parser("query")
+    q.add_argument("--project", required=True)
+    q.add_argument("--data-type", required=True)
+    q.add_argument("--out", required=True)
+    q.add_argument("--format", choices=["tsv", "json"], default="tsv")
+
+    d = sub.add_parser("download")
+    d.add_argument("--manifest", required=True)
+    d.add_argument("--out-dir", required=True)
+    d.add_argument("--processes", type=int, default=4)
+    d.add_argument("--retries", type=int, default=3)
+
+    r = sub.add_parser("run")
+    r.add_argument("--project", required=True)
+    r.add_argument("--data-type", required=True)
+    r.add_argument("--out", required=True)
+    r.add_argument("--format", choices=["tsv", "json"], default="tsv")
+    r.add_argument("--out-dir", required=True)
+    r.add_argument("--processes", type=int, default=4)
+    r.add_argument("--retries", type=int, default=3)
+
+    return parser
+
+
+def _records_from_hits(hits: list[dict]) -> list[ManifestRecord]:
+    records = []
+    for h in hits:
+        records.append(
+            ManifestRecord(
+                file_id=h["file_id"],
+                file_name=h["file_name"],
+                data_type=h["data_type"],
+                data_format=h["data_format"],
+                size=int(h["file_size"]),
+                md5=h["md5sum"],
+            )
+        )
+    return records
+
+
+def main() -> None:
+    parser = build_parser()
+    args = parser.parse_args()
+
+    if args.command in {"query", "run"}:
+        hits = query_files(args.project, args.data_type)
+        records = _records_from_hits(hits)
+        write_manifest(records, Path(args.out), fmt=args.format)
+
+    if args.command in {"download", "run"}:
+        manifest_path = Path(args.manifest if args.command == "download" else args.out)
+        run_gdc_download(manifest_path, Path(args.out_dir), args.processes, args.retries)
diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000..4ca812a
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,7 @@
+from tcga_downloader.cli import build_parser
+
+
+def test_cli_has_subcommands():
+    parser = build_parser()
+    subparsers = parser._subparsers
+    assert subparsers is not None