bunch of fixes

src/forbids/cli/init.py

@@ -48,6 +48,7 @@ def initialize(
 
     all_datatypes = bids_layout.get_datatype()
 
+    # group by instrument tags across subject, (session) and runs
     excl_ents = ["subject", "run"] + (["session"] if uniform_sessions else [])
 
     for datatype in all_datatypes:
@@ -127,18 +128,17 @@ def generate_series_model(
             )
         except ValidationError as error:
             lgr.warning(f"failed to group with {instrument_query_tags}")
-            lgr.info(error.absolute_path)
             lgr.warning(
                 f"{error.__class__.__name__} "
                 f"{'.'.join([str(e) for e in error.absolute_path])} : "
                 f"{error.message} found {error.instance if 'required' not in error.message else ''}"
             )
-            continue
+            continue  # move on to next instrument grouping
 
-        # one grouping scheme worked !
-        non_null_entities["subject"] = "ref"
+        # one instrument grouping scheme worked!
 
         # generate paths and folder
+        non_null_entities["subject"] = "ref"
         schema_path = bids_layout.build_path(non_null_entities, absolute_paths=False)
         schema_path_abs = os.path.join(bids_layout.root, schema.FORBIDS_SCHEMA_FOLDER, schema_path)
         os.makedirs(os.path.dirname(schema_path_abs), exist_ok=True)
@@ -158,3 +158,5 @@ def generate_series_model(
 
         lgr.info(f"Successfully generated schema with grouping {instrument_query_tags}")
         break
+    else:
+        raise RuntimeError("failed to generate")

src/forbids/cli/run.py

@@ -73,15 +73,11 @@ def main() -> None:
         no_error = True
         for error in validate(layout, subject=args.participant_label, session=args.session_label):
             no_error = False
-            if not isinstance(error, BIDSFileError):
-                lgr.error(error)
-
-            else:
-                lgr.error(
-                    f"{error.__class__.__name__} "
-                    f"{'.'.join(error.absolute_path)} : "
-                    f"{error.message} found {error.instance if 'required' not in error.message else ''}"
-                )
+            lgr.error(
+                f"{error.__class__.__name__} "
+                f"{'.'.join([str(pp) for pp in error.absolute_path])} : "
+                f"{error.message} found {error.instance if 'required' not in error.message else ''}"
+            )
         exit(0 if no_error else 1)
 
 

src/forbids/cli/validation.py

@@ -52,49 +52,56 @@ def validate(bids_layout: bids.BIDSLayout, **entities: dict[str, str | list]):
     )
 
     for ref_sidecar in ref_sidecars:
-        lgr.info(f"validating {ref_sidecar.relpath}")
+        lgr.info(f"validating {ref_sidecar.entities}")
         # load the schema
         sidecar_schema = ref_sidecar.get_dict()
         bidsfile_constraints = sidecar_schema.pop("bids", dict())
         query_entities = ref_sidecar.entities.copy()
 
+        for entity in schema.ALT_ENTITIES:
+            if entity not in query_entities:
+                query_entities[entity] = bids.layout.Query.NONE
         validator = schema.get_validator(sidecar_schema)
 
         for subject in subjects:
             query_entities["subject"] = subject
-            sessions = bids_layout.get_session(subject=subject, session=entities["session"])
+            sessions = bids_layout.get_session(subject=subject, session=entities["session"]) or [bids.layout.Query.NONE]
 
             for session in sessions:
+                lgr.info(f"validating sub-{subject} {'ses-'+ session if isinstance(session, str) else ''}")
                 query_entities["session"] = session
+                non_null_entities = {k: v for k, v in query_entities.items() if not isinstance(v, bids.layout.Query)}
+                expected_sidecar = bids_layout.build_path(non_null_entities, absolute_paths=False)
 
                 lgr.debug(query_entities)
 
                 sidecars_to_validate = bids_layout.get(**query_entities)
 
                 if not sidecars_to_validate and not bidsfile_constraints.get("optional", False):
-                    yield BIDSFileError(f"{ref_sidecar.relpath} found no match")
+                    yield BIDSFileError(f"{expected_sidecar}", instance="no match")
                     continue  # no point going further
 
                 num_sidecars = len(sidecars_to_validate)
                 min_runs = bidsfile_constraints.get("min_runs", 0)
                 max_runs = bidsfile_constraints.get("max_runs", 1e10)
+
                 if num_sidecars < min_runs:
                     yield BIDSFileError(
-                        f"Expected at least {min_runs} runs for {ref_sidecar.relpath}, found {num_sidecars}"
+                        f"Expected at least {min_runs} runs for {expected_sidecar}, found {num_sidecars}"
                     )
                 elif num_sidecars > max_runs:
                     yield BIDSFileError(
-                        f"Expected at most {max_runs} runs for {ref_sidecar.relpath}, found {num_sidecars}"
+                        f"Expected at most {max_runs} runs for {expected_sidecar}, found {num_sidecars}"
                     )
 
                 for sidecar in sidecars_to_validate:
                     if sidecar in all_sidecars:
                         all_sidecars.remove(sidecar)
                     else:
                         lgr.error("an error occurred")
-                    lgr.info(f"validating {sidecar.path}")
+                    lgr.debug(f"validating {sidecar.path}")
                     sidecar_data = schema.prepare_metadata(sidecar, bidsfile_constraints["instrument_tags"])
                     yield from validator.iter_errors(sidecar_data)
     for extra_sidecar in all_sidecars:
         relpath = extra_sidecar.path
-        yield BIDSFileError(f"Unexpected BIDS file{extra_sidecar.relpath}")
+        yield BIDSFileError(f"Unexpected BIDS file {extra_sidecar.relpath}")