Merge remote-tracking branch 'upstream/maint/1.10.0'

Author: effigies

src/schema/objects/formats.yaml

@@ -70,9 +70,18 @@ datetime:
   display_name: Datetime
   description: |
     A datetime in the form `"YYYY-MM-DDThh:mm:ss[.000000][Z]"`,
-    where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
-    and [Z] is an optional, valid timezone code.
-  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?'
+    where `[.000000]` is an optional subsecond resolution between 1 and 6 decimal points,
+    and `[Z]` is an optional literal character `Z` that indicates
+    Coordinated Universal Time (UTC).
+  pattern: "\
+    [0-9]{4}\
+    -(?:0[1-9]|1[0-2])\
+    -(?:0[1-9]|[12][0-9]|3[01])\
+    T(?:2[0-3]|[01][0-9])\
+    :[0-5][0-9]\
+    :(?:[0-5][0-9]|60)\
+    (?:\\.[0-9]{1,6})?\
+    Z?"
 file_relative:
   display_name: Path relative to the parent file
   description: |

src/schema/rules/files/deriv/preprocessed_data.yaml

@@ -69,6 +69,54 @@ beh_noncontinuous_common:
     space: optional
     description: optional
 
+channels_channels_common:
+  $ref: rules.files.raw.channels.channels
+  entities:
+    $ref: rules.files.raw.channels.channels.entities
+    description: optional
+
+channels_channels__meg_common:
+  $ref: rules.files.raw.channels.channels__meg
+  entities:
+    $ref: rules.files.raw.channels.channels__meg.entities
+    description: optional
+
+channels_channels__motion_common:
+  $ref: rules.files.raw.channels.channels__motion
+  entities:
+    $ref: rules.files.raw.channels.channels__motion.entities
+    description: optional
+
+channels_coordsystem_common:
+  $ref: rules.files.raw.channels.coordsystem
+  entities:
+    $ref: rules.files.raw.channels.coordsystem.entities
+    description: optional
+
+channels_coordsystem__eeg_common:
+  $ref: rules.files.raw.channels.coordsystem__eeg
+  entities:
+    $ref: rules.files.raw.channels.coordsystem__eeg.entities
+    description: optional
+
+channels_electrodes_common:
+  $ref: rules.files.raw.channels.electrodes
+  entities:
+    $ref: rules.files.raw.channels.electrodes.entities
+    description: optional
+
+channels_electrodes__meg_common:
+  $ref: rules.files.raw.channels.electrodes__meg
+  entities:
+    $ref: rules.files.raw.channels.electrodes__meg.entities
+    description: optional
+
+channels_electrodes_optodes_common:
+  $ref: rules.files.raw.channels.optodes
+  entities:
+    $ref: rules.files.raw.channels.optodes.entities
+    description: optional
+
 dwi_dwi_common:
   $ref: rules.files.raw.dwi.dwi
   entities:
@@ -229,3 +277,9 @@ pet_blood_common:
     $ref: rules.files.raw.pet.blood.entities
     space: optional
     description: optional
+
+task_events_common:
+  $ref: rules.files.raw.task.events
+  entities:
+    $ref: rules.files.raw.task.events.entities
+    description: optional

tools/schemacode/src/bidsschematools/schema.py

@@ -90,6 +90,21 @@ def _find(obj, predicate):
         yield from _find(item, predicate)
 
 
+def _dereference(namespace, base_schema):
+    # In-place, recursively dereference objects
+    # This allows a referenced object to itself contain a reference
+    # A dependency graph could be constructed, but would likely be slower
+    # to build than to duplicate a couple dereferences
+    for struct in _find(namespace, lambda obj: "$ref" in obj):
+        target = base_schema.get(struct["$ref"])
+        if target is None:
+            raise ValueError(f"Reference {struct['$ref']} not found in schema.")
+        if isinstance(target, Mapping):
+            struct.pop("$ref")
+            _dereference(target, base_schema)
+            struct.update({**target, **struct})
+
+
 def dereference(namespace, inplace=True):
     """Replace references in namespace with the contents of the referred object.
 
@@ -109,11 +124,7 @@ def dereference(namespace, inplace=True):
     if not inplace:
         namespace = deepcopy(namespace)
 
-    for struct in _find(namespace, lambda obj: "$ref" in obj):
-        target = namespace.get(struct["$ref"])
-        if isinstance(target, Mapping):
-            struct.pop("$ref")
-            struct.update({**target, **struct})
+    _dereference(namespace, namespace)
 
     # At this point, any remaining refs are one-off objects in lists
     for struct in _find(namespace, lambda obj: any("$ref" in sub for sub in obj)):

tools/schemacode/src/bidsschematools/tests/test_schema.py

@@ -85,8 +85,8 @@ def test_formats(schema_obj):
             "2022-01-05T13:16:30",
             "2022-01-05T13:16:30.5",  # subsecond resolution is allowed
             "2022-01-05T13:16:30.000005",  # up to 6 decimal points
-            "2022-01-05T13:16:30UTC",  # timezones are allowed
-            "2022-01-05T13:16:30.05UTC",
+            "2022-01-05T13:16:30Z",  # UTC indicator is allowed
+            "2022-01-05T13:16:30.05Z",
         ],
         "time": [
             "13:16:30",
@@ -133,7 +133,7 @@ def test_formats(schema_obj):
         ],
         "datetime": [
             "2022-01-05T13:16:30.1000005",  # too many decimal points
-            "2022-01-05T13:16:30U",  # time zone too short
+            "2022-01-05T13:16:30U",  # Only Z is permitted
             "2022-01-05T13:16:30UTCUTC",  # time zone too long
             "2022-01-05T34:10:10",  # invalid time
         ],