test: add CLI query smoke test

tests/test_cli.py

@@ -5,3 +5,34 @@ def test_cli_has_subcommands():
     parser = build_parser()
     subparsers = parser._subparsers
     assert subparsers is not None
+
+from unittest.mock import patch
+
+from tcga_downloader.cli import main
+
+
+def test_cli_query_writes_manifest(tmp_path, monkeypatch):
+    args = [
+        "tcga-downloader",
+        "query",
+        "--project",
+        "TCGA-BRCA",
+        "--data-type",
+        "Gene Expression",
+        "--out",
+        str(tmp_path / "m.tsv"),
+    ]
+    monkeypatch.setattr("sys.argv", args)
+    with patch("tcga_downloader.cli.query_files") as q:
+        q.return_value = [
+            {
+                "file_id": "f1",
+                "file_name": "a.tsv",
+                "data_type": "Gene Expression",
+                "data_format": "TSV",
+                "file_size": 123,
+                "md5sum": "abc",
+            }
+        ]
+        main()
+    assert (tmp_path / "m.tsv").exists()