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SCHEMA: Update references to use _ref instead of $ref #1082

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SCHEMA: Update references to use _ref instead of $ref #1082

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8 changes: 4 additions & 4 deletions src/schema/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -316,14 +316,14 @@ ExampleField:
```

Furthermore, if the data type description of a field is reused across fields,
then it may be defined in a separate field and referenced in each target field with the `$ref` keyword.
Here is an example of a field definition using `$ref`:
then it may be defined in a separate field and referenced in each target field with the `_ref` keyword.
Here is an example of a field definition using `_ref`:
```yaml
ExampleField:
name: ExampleField
description: |
The description of "ExampleField".
$ref: _ReferenceField
_ref: _ReferenceField
```
The target field (`_ReferenceField` in this case) MUST be located in
the metadata YAML file, and MUST contain all information
Expand All @@ -341,7 +341,7 @@ _ReferenceField:
- PossibleValue2
```

The result of including `$ref` makes the `ExampleField` above equivalent to the following format:
The result of including `_ref` makes the `ExampleField` above equivalent to the following format:
```yaml
ExampleField:
name: ExampleField
Expand Down
74 changes: 37 additions & 37 deletions src/schema/objects/metadata.yaml
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Expand Up @@ -66,10 +66,10 @@ AnatomicalLandmarkCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`"AnatomicalLandmarkCoordinateSystemDescription"`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
AnatomicalLandmarkCoordinateSystemDescription:
name: AnatomicalLandmarkCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -552,10 +552,10 @@ DigitizedHeadPointsCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`"DigitizedHeadPointsCoordinateSystemDescription"`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
DigitizedHeadPointsCoordinateSystemDescription:
name: DigitizedHeadPointsCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -642,10 +642,10 @@ EEGCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`EEGCoordinateSystemDescription`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
EEGCoordinateSystemDescription:
name: EEGCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -828,10 +828,10 @@ FiducialsCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`"FiducialsCoordinateSystemDescription"`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
FiducialsCoordinateSystemDescription:
name: FiducialsCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -961,10 +961,10 @@ GeneticLevel:
Values MUST be one of `"Genetic"`, `"Genomic"`, `"Epigenomic"`,
`"Transcriptomic"`, `"Metabolomic"`, or `"Proteomic"`.
anyOf:
- $ref: _GeneticLevelEnum
- _ref: _GeneticLevelEnum
- type: array
items:
$ref: _GeneticLevelEnum
_ref: _GeneticLevelEnum
Genetics.Database:
name: Genetics.Database
description: |
Expand Down Expand Up @@ -998,11 +998,11 @@ Genetics:
type: object
properties:
Database:
$ref: Genetics.Database
_ref: Genetics.Database
Dataset:
$ref: Genetics.Dataset
_ref: Genetics.Dataset
Descriptors:
$ref: Genetics.Descriptors
_ref: Genetics.Descriptors
GradientSetType:
name: GradientSetType
description: |
Expand Down Expand Up @@ -1072,10 +1072,10 @@ HeadCoilCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`HeadCoilCoordinateSystemDescription`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
HeadCoilCoordinateSystemDescription:
name: HeadCoilCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -1492,10 +1492,10 @@ MEGCoordinateSystem:
If `"Other"`, provide definition of the coordinate system in
`"MEGCoordinateSystemDescription"`.
anyOf:
- $ref: _MEGCoordSys
- $ref: _EEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _MEGCoordSys
- _ref: _EEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
MEGCoordinateSystemDescription:
name: MEGCoordinateSystemDescription
description: |
Expand Down Expand Up @@ -2622,15 +2622,15 @@ StimulusPresentation:
type: object
properties:
OperatingSystem:
$ref: OperatingSystem
_ref: OperatingSystem
SoftwareName:
$ref: SoftwareName
_ref: SoftwareName
SoftwareRRID:
$ref: SoftwareRRID
_ref: SoftwareRRID
SoftwareVersion:
$ref: SoftwareVersion
_ref: SoftwareVersion
Code:
$ref: Code
_ref: Code
SubjectArtefactDescription:
name: SubjectArtefactDescription
description: |
Expand Down Expand Up @@ -2945,9 +2945,9 @@ iEEGCoordinateSystem:
[2D coordinate systems](/04-modality-specific-files/04-intracranial\
-electroencephalography.html#allowed-2d-coordinate-systems).
anyOf:
- $ref: _iEEGCoordSys
- $ref: _StandardTemplateCoordSys
- $ref: _StandardTemplateDeprecatedCoordSys
- _ref: _iEEGCoordSys
- _ref: _StandardTemplateCoordSys
- _ref: _StandardTemplateDeprecatedCoordSys
iEEGCoordinateSystemDescription:
name: iEEGCoordinateSystemDescription
description: |
Expand Down
12 changes: 6 additions & 6 deletions tools/schemacode/schemacode/schema.py
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Expand Up @@ -21,17 +21,17 @@ def _get_entry_name(path):
return path.name


def dereference_yaml(schema, struct):
"""Recursively search a dictionary-like object for $ref keys.
def dereference_yaml(schema, struct, ref_key="_ref"):
"""Recursively search a dictionary-like object for _ref keys.

Each $ref key is replaced with the contents of the referenced field in the overall
Each _ref key is replaced with the contents of the referenced field in the overall
dictionary-like object.
"""
if isinstance(struct, dict):
if "$ref" in struct:
ref_field = struct["$ref"]
if ref_key in struct:
ref_field = struct[ref_key]
template = schema[ref_field]
struct.pop("$ref")
struct.pop(ref_key)
# Result is template object with local overrides
struct = {**template, **struct}

Expand Down