Merge branch 'main' into list-metadata

cubids/cli.py

@@ -121,6 +121,7 @@ def _parse_validate():
         allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
+    IsFile = partial(_is_file, parser=parser)
 
     parser.add_argument(
         "bids_dir",
@@ -177,6 +178,17 @@ def _parse_validate():
         help="Lets user run a locally installed BIDS validator. Default is set to False ",
         required=False,
     )
+    parser.add_argument(
+        "--schema",
+        type=IsFile,
+        action="store",
+        default=None,
+        help=(
+            "Path to a BIDS schema JSON file. "
+            "Default is None, which uses the latest schema available to the validator."
+        ),
+        required=False,
+    )
     return parser
 
 
@@ -243,6 +255,7 @@ def _parse_bids_version():
         allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
+    IsFile = partial(_is_file, parser=parser)
 
     parser.add_argument(
         "bids_dir",
@@ -263,6 +276,17 @@ def _parse_bids_version():
             "By default, `cubids bids-version /bids/path` prints to the terminal."
         ),
     )
+    parser.add_argument(
+        "--schema",
+        type=IsFile,
+        action="store",
+        default=None,
+        help=(
+            "Path to a BIDS schema JSON file. "
+            "Default is None, which uses the latest schema available to the validator."
+        ),
+        required=False,
+    )
     return parser
 
 
@@ -412,6 +436,7 @@ def _parse_group():
         allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
+    IsFile = partial(_is_file, parser=parser)
 
     parser.add_argument(
         "bids_dir",
@@ -446,13 +471,24 @@ def _parse_group():
     parser.add_argument(
         "--config",
         action="store",
-        type=PathExists,
+        type=IsFile,
         default=None,
         help=(
             "Path to a config file for grouping. "
             "If not provided, then the default config file from CuBIDS will be used."
         ),
     )
+    parser.add_argument(
+        "--schema",
+        type=IsFile,
+        action="store",
+        default=None,
+        help=(
+            "Path to a BIDS schema JSON file. "
+            "Default is None, which uses the latest schema available to the validator."
+        ),
+        required=False,
+    )
     return parser
 
 
@@ -601,6 +637,17 @@ def _parse_apply():
             "If not provided, then the default config file from CuBIDS will be used."
         ),
     )
+    parser.add_argument(
+        "--schema",
+        type=IsFile,
+        action="store",
+        default=None,
+        help=(
+            "Path to a BIDS schema JSON file. "
+            "Default is None, which uses the latest schema available to the validator."
+        ),
+        required=False,
+    )
 
     return parser
 

cubids/config.py

@@ -26,3 +26,32 @@ def load_config(config_file):
         config = yaml.safe_load(f)
 
     return config
+
+
+def load_schema(schema_file):
+    """Load a JSON file containing the BIDS schema.
+
+    Parameters
+    ----------
+    schema_file : str or pathlib.Path, optional
+        The path to the schema file. If None, the default schema file is used.
+
+    Returns
+    -------
+    dict
+        The schema loaded from the YAML file.
+    """
+    import json
+
+    if schema_file is None:
+        schema_file = Path(importlib.resources.files("cubids") / "data/schema.json")
+
+    with schema_file.open() as f:
+        schema = json.load(f)
+
+    print(
+        f"Loading BIDS schema version: {schema['schema_version']}. "
+        f"BIDS version: {schema['bids_version']}"
+    )
+
+    return schema

cubids/cubids.py

@@ -25,7 +25,7 @@
 from tqdm import tqdm
 
 from cubids import utils
-from cubids.config import load_config
+from cubids.config import load_config, load_schema
 from cubids.constants import NON_KEY_ENTITIES
 from cubids.metadata_merge import check_merging_operations, group_by_acquisition_sets
 
@@ -51,6 +51,9 @@ class CuBIDS(object):
     force_unlock : :obj:`bool`, optional
         If True, force unlock all files in the BIDS dataset.
         Default is False.
+    schema_json : :obj:`str`, optional
+        Path to a BIDS schema JSON file.
+        Default is None, in which case the default schema in CuBIDS is used.
 
     Attributes
     ----------
@@ -88,6 +91,8 @@ class CuBIDS(object):
         A data dictionary for TSV outputs.
     use_datalad : :obj:`bool`
         If True, use datalad to track changes to the BIDS dataset.
+    schema : :obj:`dict`
+        The BIDS schema dictionary.
     is_longitudinal : :obj:`bool`
         If True, adds "ses" in filepath.
     """
@@ -99,6 +104,7 @@ def __init__(
         acq_group_level="subject",
         grouping_config=None,
         force_unlock=False,
+        schema_json=None,
     ):
         self.path = os.path.abspath(data_root)
         self._layout = None
@@ -116,6 +122,7 @@ def __init__(
         self.cubids_code_dir = Path(self.path + "/code/CuBIDS").is_dir()
         self.data_dict = {}  # data dictionary for TSV outputs
         self.use_datalad = use_datalad  # True if flag set, False if flag unset
+        self.schema = load_schema(schema_json)
         self.is_longitudinal = self._infer_longitudinal()  # inferred from dataset structure
 
         if self.use_datalad:
@@ -546,8 +553,9 @@ def change_filename(self, filepath, entities):
         """
         new_path = utils.build_path(
             filepath=filepath,
-            entities=entities,
+            out_entities=entities,
             out_dir=str(self.path),
+            schema=self.schema,
             is_longitudinal=self.is_longitudinal,
         )