From be6bbc6a24d9dcd52a4054f5d90584bcbbd92045 Mon Sep 17 00:00:00 2001 From: Jason Kai Date: Tue, 17 Sep 2024 19:06:06 -0400 Subject: [PATCH 1/2] Update conditions when dataset_description created Only create during participant runs if file doesn't already exist or if overwrite is True. --- src/niftyone/__main__.py | 3 +- src/niftyone/metadata/bids.py | 8 +- tests/unit/niftyone/metadata/test_bids.py | 7 +- uv.lock | 2623 +++++++++++++++++++++ 4 files changed, 2634 insertions(+), 7 deletions(-) create mode 100644 uv.lock diff --git a/src/niftyone/__main__.py b/src/niftyone/__main__.py index 1cfabe8..067b69d 100644 --- a/src/niftyone/__main__.py +++ b/src/niftyone/__main__.py @@ -19,10 +19,9 @@ def main() -> None: out_dir = Path(args.out_dir) out_dir.mkdir(exist_ok=True, parents=True) - bids.make_dataset_description(out_dir=out_dir) - match args.analysis_level: case "participant": + bids.make_dataset_description(out_dir=out_dir, overwrite=args.overwrite) analysis_levels.participant( bids_dir=args.bids_dir, out_dir=out_dir, diff --git a/src/niftyone/metadata/bids.py b/src/niftyone/metadata/bids.py index 0bb39ea..9bd5767 100644 --- a/src/niftyone/metadata/bids.py +++ b/src/niftyone/metadata/bids.py @@ -6,7 +6,7 @@ import niftyone -def make_dataset_description(out_dir: Path) -> None: +def make_dataset_description(out_dir: Path, overwrite: bool) -> None: """Create dataset_description.json for BIDS dataset.""" description = { "Name": "NiftyOne", @@ -23,5 +23,7 @@ def make_dataset_description(out_dir: Path) -> None: "License": "LGPL-2.1", } - with (out_dir / "dataset_description.json").open("w") as f: - json.dump(description, f, indent=4) + ds_fpath = out_dir.joinpath("dataset_description.json") + if not ds_fpath.exists() or overwrite: + with ds_fpath.open("w") as f: + json.dump(description, f, indent=4) diff --git a/tests/unit/niftyone/metadata/test_bids.py b/tests/unit/niftyone/metadata/test_bids.py index 9104ac7..4905ed0 100644 --- a/tests/unit/niftyone/metadata/test_bids.py +++ b/tests/unit/niftyone/metadata/test_bids.py @@ -1,13 +1,16 @@ import json from pathlib import Path +import pytest + import niftyone from niftyone.metadata import bids -def test_make_dataset_description(tmp_path: Path) -> None: +@pytest.mark.parametrize("overwrite", [(True), (False)]) +def test_make_dataset_description(tmp_path: Path, overwrite: bool) -> None: out_dir = tmp_path - bids.make_dataset_description(out_dir=out_dir) + bids.make_dataset_description(out_dir=out_dir, overwrite=overwrite) # Check file created json_fpath = out_dir / "dataset_description.json" diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..4261bb6 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2623 @@ +version = 1 +requires-python = ">=3.10" +resolution-markers = [ + "python_full_version < '3.11' and platform_system == 'Darwin'", + "python_full_version < '3.11' and platform_machine == 'aarch64' and platform_system == 'Linux'", + "(python_full_version < 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