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Merge branch 'master' into issue-914-dev
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‎.pre-commit-config.yaml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ repos:
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- id: check-added-large-files
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- id: check-case-conflict
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- repo: https://github.com/python-jsonschema/check-jsonschema
20-
rev: 0.31.0
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rev: 0.31.1
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hooks:
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- id: check-dependabot
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- id: check-github-workflows
@@ -27,7 +27,7 @@ repos:
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- id: check-readthedocs
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files: readthedocs.yml
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- repo: https://github.com/psf/black
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rev: 24.10.0
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rev: 25.1.0
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hooks:
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- id: black
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files: ^tools/(?!schemacode)
@@ -37,7 +37,7 @@ repos:
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files: tools/schemacode
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args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
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- repo: https://github.com/pyCQA/isort
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rev: 5.13.2
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rev: 6.0.0
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hooks:
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- id: isort
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files: ^tools/(?!schemacode)
@@ -69,7 +69,7 @@ repos:
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- id: pretty-format-toml
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args: [--autofix, --indent, '4', --no-sort]
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.0
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rev: v2.4.1
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hooks:
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- id: codespell
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args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]

‎src/schema/objects/formats.yaml‎

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -70,9 +70,18 @@ datetime:
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display_name: Datetime
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description: |
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A datetime in the form `"YYYY-MM-DDThh:mm:ss[.000000][Z]"`,
73-
where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
74-
and [Z] is an optional, valid timezone code.
75-
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})?'
73+
where `[.000000]` is an optional subsecond resolution between 1 and 6 decimal points,
74+
and `[Z]` is an optional literal character `Z` that indicates
75+
Coordinated Universal Time (UTC).
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pattern: "\
77+
[0-9]{4}\
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-(?:0[1-9]|1[0-2])\
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-(?:0[1-9]|[12][0-9]|3[01])\
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T(?:2[0-3]|[01][0-9])\
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:[0-5][0-9]\
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:(?:[0-5][0-9]|60)\
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(?:\\.[0-9]{1,6})?\
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Z?"
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file_relative:
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display_name: Path relative to the parent file
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description: |

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

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -69,6 +69,54 @@ beh_noncontinuous_common:
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space: optional
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description: optional
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72+
channels_channels_common:
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$ref: rules.files.raw.channels.channels
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entities:
75+
$ref: rules.files.raw.channels.channels.entities
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description: optional
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78+
channels_channels__meg_common:
79+
$ref: rules.files.raw.channels.channels__meg
80+
entities:
81+
$ref: rules.files.raw.channels.channels__meg.entities
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description: optional
83+
84+
channels_channels__motion_common:
85+
$ref: rules.files.raw.channels.channels__motion
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entities:
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$ref: rules.files.raw.channels.channels__motion.entities
88+
description: optional
89+
90+
channels_coordsystem_common:
91+
$ref: rules.files.raw.channels.coordsystem
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entities:
93+
$ref: rules.files.raw.channels.coordsystem.entities
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description: optional
95+
96+
channels_coordsystem__eeg_common:
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$ref: rules.files.raw.channels.coordsystem__eeg
98+
entities:
99+
$ref: rules.files.raw.channels.coordsystem__eeg.entities
100+
description: optional
101+
102+
channels_electrodes_common:
103+
$ref: rules.files.raw.channels.electrodes
104+
entities:
105+
$ref: rules.files.raw.channels.electrodes.entities
106+
description: optional
107+
108+
channels_electrodes__meg_common:
109+
$ref: rules.files.raw.channels.electrodes__meg
110+
entities:
111+
$ref: rules.files.raw.channels.electrodes__meg.entities
112+
description: optional
113+
114+
channels_electrodes_optodes_common:
115+
$ref: rules.files.raw.channels.optodes
116+
entities:
117+
$ref: rules.files.raw.channels.optodes.entities
118+
description: optional
119+
72120
dwi_dwi_common:
73121
$ref: rules.files.raw.dwi.dwi
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entities:
@@ -229,3 +277,9 @@ pet_blood_common:
229277
$ref: rules.files.raw.pet.blood.entities
230278
space: optional
231279
description: optional
280+
281+
task_events_common:
282+
$ref: rules.files.raw.task.events
283+
entities:
284+
$ref: rules.files.raw.task.events.entities
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description: optional

‎tools/schemacode/src/bidsschematools/schema.py‎

Lines changed: 16 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -90,6 +90,21 @@ def _find(obj, predicate):
9090
yield from _find(item, predicate)
9191

9292

93+
def _dereference(namespace, base_schema):
94+
# In-place, recursively dereference objects
95+
# This allows a referenced object to itself contain a reference
96+
# A dependency graph could be constructed, but would likely be slower
97+
# to build than to duplicate a couple dereferences
98+
for struct in _find(namespace, lambda obj: "$ref" in obj):
99+
target = base_schema.get(struct["$ref"])
100+
if target is None:
101+
raise ValueError(f"Reference {struct['$ref']} not found in schema.")
102+
if isinstance(target, Mapping):
103+
struct.pop("$ref")
104+
_dereference(target, base_schema)
105+
struct.update({**target, **struct})
106+
107+
93108
def dereference(namespace, inplace=True):
94109
"""Replace references in namespace with the contents of the referred object.
95110
@@ -109,11 +124,7 @@ def dereference(namespace, inplace=True):
109124
if not inplace:
110125
namespace = deepcopy(namespace)
111126

112-
for struct in _find(namespace, lambda obj: "$ref" in obj):
113-
target = namespace.get(struct["$ref"])
114-
if isinstance(target, Mapping):
115-
struct.pop("$ref")
116-
struct.update({**target, **struct})
127+
_dereference(namespace, namespace)
117128

118129
# At this point, any remaining refs are one-off objects in lists
119130
for struct in _find(namespace, lambda obj: any("$ref" in sub for sub in obj)):

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

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -85,8 +85,8 @@ def test_formats(schema_obj):
8585
"2022-01-05T13:16:30",
8686
"2022-01-05T13:16:30.5", # subsecond resolution is allowed
8787
"2022-01-05T13:16:30.000005", # up to 6 decimal points
88-
"2022-01-05T13:16:30UTC", # timezones are allowed
89-
"2022-01-05T13:16:30.05UTC",
88+
"2022-01-05T13:16:30Z", # UTC indicator is allowed
89+
"2022-01-05T13:16:30.05Z",
9090
],
9191
"time": [
9292
"13:16:30",
@@ -133,7 +133,7 @@ def test_formats(schema_obj):
133133
],
134134
"datetime": [
135135
"2022-01-05T13:16:30.1000005", # too many decimal points
136-
"2022-01-05T13:16:30U", # time zone too short
136+
"2022-01-05T13:16:30U", # Only Z is permitted
137137
"2022-01-05T13:16:30UTCUTC", # time zone too long
138138
"2022-01-05T34:10:10", # invalid time
139139
],

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