add --force mode for metadata.yml file

.github/workflows/tests.yml

@@ -44,7 +44,14 @@ jobs:
         -   name: Install package
             run: pip install .[test]
 
+        -   uses: actions/cache@v4
+            id: cache
+            with:
+                path: /home/runner/work/eye2bids/eye2bids/tests/data/osf
+                key: data
+
         -   name: Install data
+            if: ${{ steps.cache.outputs.cache-hit != 'true' }}
             run: make test_data
 
         -   name: unit tests

README.md

@@ -1,3 +1,5 @@
+[![test](https://github.com/bids-standard/eye2bids/actions/workflows/tests.yml/badge.svg)](https://github.com/bids-standard/eye2bids/actions/workflows/tests.yml)
+
 # eye2bids
 
 ## Installation

eye2bids/_cli.py

@@ -55,4 +55,5 @@ def cli(argv: Sequence[str] = sys.argv) -> None:
         metadata_file=metadata_file,
         output_dir=output_dir,
         interactive=args.interactive,
+        force=args.force,
     )

eye2bids/_parser.py

@@ -70,4 +70,13 @@ def global_parser() -> ArgumentParser:
         type=int,
         nargs=2,
     )
+    parser.add_argument(
+        "-f",
+        "--force",
+        help="""
+        To run the converter without passing a metadata.yml file.\n
+        Creates an invalid BIDS dataset.
+        """,
+        action="store_true",
+    )
     return parser

eye2bids/edf2bids.py

@@ -26,6 +26,7 @@ def _check_inputs(
     metadata_file: str | Path | None = None,
     output_dir: str | Path | None = None,
     interactive: bool = False,
+    force: bool = False,
 ) -> tuple[Path, Path | None, Path]:
     """Check if inputs are valid."""
     if input_file is None:
@@ -45,16 +46,34 @@ def _check_inputs(
         raise FileNotFoundError(f"No such input file: {cheked_input_file}")
 
     if metadata_file in [None, ""] and interactive:
-        e2b_log.info(
+        e2b_log.warning(
             """Load the metadata.yml file with the additional metadata.\n
-            This file must contain at least the additional REQUIRED metadata
+            You can find a template in the eye2bids GitHub.\n
+            This file must contain at least the additional REQUIRED metadata\n
             in the format specified in the BIDS specification.\n"""
         )
         metadata_file = Prompt.ask("Enter the file path to the metadata.yml file")
 
-    if metadata_file in ["", None]:
-        checked_metadata_file = None
-    elif isinstance(metadata_file, str):
+    if metadata_file in [None, ""]:
+        if not force:
+            e2b_log.error(
+                """You didn't pass a metadata.yml file.
+                As this file contains metadata
+                which is REQUIRED for a valid BIDS dataset,
+                the conversion process now stops.
+                Please start again with a metadata.yml file
+                or run eye2bids in --force mode.\n
+                This will produce an invalid BIDS dataset.\n"""
+            )
+            raise SystemExit(1)
+        else:
+            e2b_log.warning(
+                """You didn't pass a metadata.yml file.
+                    Note that this will produce an invalid BIDS dataset.\n"""
+            )
+
+    checked_metadata_file = None
+    if isinstance(metadata_file, str):
         checked_metadata_file = Path(metadata_file)
     elif isinstance(metadata_file, Path):
         checked_metadata_file = metadata_file
@@ -484,13 +503,14 @@ def edf2bids(
     metadata_file: str | Path | None = None,
     output_dir: str | Path | None = None,
     interactive: bool = False,
+    force: bool = False,
 ) -> None:
     """Convert edf to tsv + json."""
     if not _check_edf2asc_present():
         return
 
     input_file, metadata_file, output_dir = _check_inputs(
-        input_file, metadata_file, output_dir, interactive
+        input_file, metadata_file, output_dir, interactive, force
     )
 
     # CONVERSION events

pyproject.toml

@@ -114,6 +114,6 @@ module = [
 ]
 
 [tool.pytest.ini_options]
-addopts = "-ra -q -vv --cov eye2bids"
+addopts = "-ra -q -vv --cov eye2bids --durations=0"
 norecursedirs = "data"
 testpaths = ["tests/"]

tests/test_cli.py

@@ -16,23 +16,25 @@ def root_dir() -> Path:
 
 
 @pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
-@pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
 @pytest.mark.parametrize("output_dir", [data_dir() / "output", None])
 @pytest.mark.parametrize("use_relative_path", [False, True])
-def test_edf_cli(use_relative_path, metadata_file, output_dir, eyelink_test_data_dir):
+def test_edf_cli(use_relative_path, output_dir, eyelink_test_data_dir):
+
+    metadata_file = data_dir() / "metadata.yml"
+
     input_dir = eyelink_test_data_dir / "satf"
     input_file = edf_test_files(input_dir=input_dir)[0]
 
     if use_relative_path:
         input_file = input_file.relative_to(root_dir())
+        metadata_file = metadata_file.relative_to(root_dir())
 
-    command = ["eye2bids", "--input_file", str(input_file)]
-    if metadata_file is not None:
-        if use_relative_path:
-            metadata_file = metadata_file.relative_to(root_dir())
-        metadata_file = str(metadata_file)
-        command.extend(["--metadata_file", metadata_file])
-
+    command = [
+        "eye2bids",
+        "--input_file",
+        str(input_file),
+        *["--metadata_file", str(metadata_file)],
+    ]
     if output_dir is not None:
         if use_relative_path:
             output_dir = output_dir.relative_to(root_dir())
@@ -53,5 +55,6 @@ def test_all_edf_files(input_file):
         str(input_file),
         "--output_dir",
         str(data_dir() / "output"),
+        "--force",
     ]
     cli(command)

tests/test_edf2bids.py

@@ -48,8 +48,9 @@ def _check_output_exists(output_dir, input_file, eye=1):
 
 
 @pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
-@pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
-def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
+def test_edf_end_to_end(eyelink_test_data_dir):
+    metadata_file = data_dir() / "metadata.yml"
+
     input_dir = eyelink_test_data_dir / "satf"
     input_file = edf_test_files(input_dir=input_dir)[0]
 
@@ -75,8 +76,28 @@ def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
 
 
 @pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
-@pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
-def test_edf_end_to_end_2eyes(metadata_file, eyelink_test_data_dir):
+def test_edf_end_to_end_error_no_metadata(eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / "2eyes"
+    input_file = edf_test_files(input_dir=input_dir)[0]
+
+    output_dir = data_dir() / "output"
+    output_dir.mkdir(exist_ok=True)
+
+    # when force is true no system exit even with no metadata file
+    edf2bids(input_file=input_file, metadata_file=None, output_dir=output_dir, force=True)
+    # but when force is false, no metadata file triggers a failure
+    with pytest.raises(SystemExit) as pytest_wrapped_e:
+        edf2bids(
+            input_file=input_file, metadata_file=None, output_dir=output_dir, force=False
+        )
+        assert pytest_wrapped_e.type == SystemExit
+        assert pytest_wrapped_e.value.code == 1
+
+
+@pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
+def test_edf_end_to_end_2eyes(eyelink_test_data_dir):
+    metadata_file = data_dir() / "metadata.yml"
+
     input_dir = eyelink_test_data_dir / "2eyes"
     input_file = edf_test_files(input_dir=input_dir)[0]
 
@@ -123,7 +144,7 @@ def test_edf_nan_in_tsv(eyelink_test_data_dir):
     output_dir = data_dir() / "output"
     output_dir.mkdir(exist_ok=True)
 
-    edf2bids(input_file=input_file, output_dir=output_dir)
+    edf2bids(input_file=input_file, output_dir=output_dir, force=True)
 
     expected_eyetrack_tsv = output_dir / f"{input_file.stem}_recording-eye1_physio.tsv.gz"
     df = pd.read_csv(expected_eyetrack_tsv, sep="\t", header=None)
@@ -144,7 +165,7 @@ def test_number_columns_2eyes_tsv(eyelink_test_data_dir):
     output_dir = data_dir() / "output"
     output_dir.mkdir(exist_ok=True)
 
-    edf2bids(input_file=input_file, output_dir=output_dir)
+    edf2bids(input_file=input_file, output_dir=output_dir, force=True)
 
     expected_eyetrack_tsv = output_dir / f"{input_file.stem}_recording-eye1_physio.tsv.gz"
     df = pd.read_csv(expected_eyetrack_tsv, sep="\t")
@@ -165,7 +186,7 @@ def test_number_columns_1eye_tsv(eyelink_test_data_dir):
     output_dir = data_dir() / "output"
     output_dir.mkdir(exist_ok=True)
 
-    edf2bids(input_file=input_file, output_dir=output_dir)
+    edf2bids(input_file=input_file, output_dir=output_dir, force=True)
 
     expected_eyetrack_tsv = output_dir / f"{input_file.stem}_recording-eye1_physio.tsv.gz"
     df = pd.read_csv(expected_eyetrack_tsv, sep="\t")
@@ -469,7 +490,7 @@ def test_number_columns_physioevents_tsv(eyelink_test_data_dir):
     output_dir = data_dir() / "output"
     output_dir.mkdir(exist_ok=True)
 
-    edf2bids(input_file=input_file, output_dir=output_dir)
+    edf2bids(input_file=input_file, output_dir=output_dir, force=True)
 
     expected_physioevents_tsv = (
         output_dir / f"{input_file.stem}_recording-eye2_physioevents.tsv.gz"
@@ -528,7 +549,7 @@ def test_physioevents_value(folder, expected, eyelink_test_data_dir):
     output_dir = data_dir() / "output"
     output_dir.mkdir(exist_ok=True)
 
-    edf2bids(input_file=input_file, output_dir=output_dir)
+    edf2bids(input_file=input_file, output_dir=output_dir, force=True)
 
     expected_eyetrackphysio_tsv = (
         output_dir / f"{input_file.stem}_recording-eye1_physioevents.tsv.gz"

tools/download_test_data.py

@@ -15,6 +15,8 @@
 
 output_dir = root_dir / "tests" / "data" / "osf"
 
+print(f"Saving files to {output_dir}")
+
 if output_dir.exists():
     shutil.rmtree(output_dir)
 output_dir.mkdir(parents=True)