add script to detect deprecated bids URI in intended for

.gitignore

@@ -12,4 +12,6 @@ env/
 
 *.asv
 
-site/
+site/
+
+deprecated_intended_for.log

ieeg_epilepsy/derivatives/brainvisa/dataset_description.json

@@ -0,0 +1,5 @@
+{
+ "Name": "Brainvisa dertivatives",
+ "DatasetType": "derivative",
+ "BIDSVersion": "1.7.0"
+}

ieeg_epilepsyNWB/derivatives/brainvisa/dataset_description.json

@@ -0,0 +1,5 @@
+{
+ "Name": "Brainvisa dertivatives",
+ "DatasetType": "derivative",
+ "BIDSVersion": "1.7.0"
+}

tools/check_intended_for.py

@@ -0,0 +1,71 @@
+"""Check jsons of all datasets for IntendedFor field.
+
+Make sure that the format is not one of the deprecated ones.
+
+https://bids-specification.readthedocs.io/en/latest/common-principles.html#bids-uri
+
+Example:
+
+- bad
+
+ .. code-block:: json
+
+ "IntendedFor": ["anat/sub-01_T1w.nii.gz"]
+
+
+- good
+
+ .. code-block:: json
+
+ "IntendedFor": ["bids::sub-01/anat/sub-01_T1w.nii.gz"]
+"""
+
+from pathlib import Path
+import json
+from warnings import warn
+from rich import print
+
+VERBOSE = False
+
+root_dir = Path(__file__).parent.parent
+
+deprecated_formats = {}
+
+for json_path in root_dir.glob("**/*.json"):
+
+ if VERBOSE:
+ print(f"Checking {json_path.relative_to(root_dir)}")
+
+ with open(json_path) as f:
+ content = json.load(f)
+
+ if "IntendedFor" in content:
+ intended_for = content["IntendedFor"]
+ if isinstance(intended_for, str):
+ intended_for = [intended_for]
+
+ for intended_for_path in intended_for:
+ if not intended_for_path.startswith("bids"):
+ if json_path not in deprecated_formats:
+ deprecated_formats[json_path] = []
+ deprecated_formats[json_path].append(intended_for_path)
+
+if deprecated_formats:
+
+ log_file = root_dir / "deprecated_intended_for.log"
+
+ with open(log_file, "w") as f:
+ for json_path, deprecated_paths in deprecated_formats.items():
+ f.write(f"{json_path.relative_to(root_dir)}\n")
+ print(f"{json_path.relative_to(root_dir)}")
+ for deprecated_path in deprecated_paths:
+ f.write(f" {deprecated_path}\n")
+ print(f" {deprecated_path}")
+
+ raise(ValueError)(
+ f"Found {len(deprecated_formats)} jsons with deprecated IntendedFor formats.\n"
+ f"See {log_file}\n"
+ "Please update them to the new format.\n"
+ "See https://bids-specification.readthedocs.io/en/latest/common-principles.html#bids-uri"
+ )
+

tools/requirements.txt

@@ -1,3 +1,4 @@
 pybids 
 pandas
-tabulate
+tabulate
+rich