rf(schema): Consolidate rules.dataset_metadata under rules.json

src/derivatives/atlas.md

@@ -220,12 +220,14 @@ corresponding to the atlas or atlases in the structure.
 Atlas metadata fields:
 
 <!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/json
 The definitions of these fields can be found in
   src/schema/objects/metadata.yaml
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_json_table('dataset_metadata.atlas_description') }}
+{{ MACROS___make_json_table('json.atlas.atlas_description') }}
 
 Example `atlas-MyAtlas2025_description.json`:
 

src/metaschema.json

@@ -459,9 +459,6 @@
           "type": "array",
           "items": { "type": "string" }
         },
-        "dataset_metadata": {
-          "type": "object"
-        },
         "directories": {
           "type": "object"
         },
@@ -513,7 +510,6 @@
         "tabular_data",
         "metaentities",
         "common_principles",
-        "dataset_metadata",
         "directories",
         "errors",
         "modalities"

src/modality-agnostic-files/dataset-description.md

@@ -19,12 +19,14 @@ A guide for using macros can be found at
 Every dataset MUST include this file with the following fields:
 
 <!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/json
 The definitions of these fields can be found in
   src/schema/objects/metadata.yaml
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_json_table('dataset_metadata.dataset_description') }}
+{{ MACROS___make_json_table('json.dataset.dataset_description') }}
 
 Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
 and OPTIONAL keys:

src/modality-specific-files/electroencephalography.md

@@ -384,7 +384,7 @@ General fields:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -396,7 +396,7 @@ Fields relating to the EEG electrode positions:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -408,7 +408,7 @@ Fields relating to the position of fiducials measured during an EEG session/run:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -420,7 +420,7 @@ Fields relating to the position of anatomical landmark measured during an EEG se
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at

src/modality-specific-files/electromyography.md

@@ -533,7 +533,7 @@ Fields relating to the EMG coordinate system(s):
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at

src/modality-specific-files/genetic-descriptor.md

@@ -94,21 +94,14 @@ A guide for using macros can be found at
 {{ MACROS___render_text("objects.files.genetic_info.description") }}
 
 <!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/json
 The definitions of these fields can be found in
   src/schema/objects/metadata.yaml
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_metadata_table(
-   {
-      "GeneticLevel": "REQUIRED",
-      "AnalyticalApproach": "OPTIONAL",
-      "SampleOrigin": "REQUIRED",
-      "TissueOrigin": "OPTIONAL",
-      "BrainLocation": "OPTIONAL",
-      "CellType": "OPTIONAL",
-   }
-) }}
+{{ MACROS___make_json_table("json.genetics.genetic_info") }}
 
 To ensure dataset description consistency, we recommend following [Multi-omics approaches to disease](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1215-1) by Hasin et al. 2017 to determine the `GeneticLevel:`
 

src/modality-specific-files/intracranial-electroencephalography.md

@@ -383,7 +383,7 @@ General fields:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -395,7 +395,7 @@ Fields relating to the iEEG electrode positions:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at

src/modality-specific-files/magnetoencephalography.md

@@ -337,7 +337,7 @@ MEG and EEG sensors:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -349,7 +349,7 @@ Head localization coils:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -361,7 +361,7 @@ Digitized head points:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -373,7 +373,7 @@ Anatomical MRI:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -385,7 +385,7 @@ Anatomical landmarks:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -413,7 +413,7 @@ Fiducials information:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at

src/modality-specific-files/near-infrared-spectroscopy.md

@@ -387,7 +387,7 @@ General fields:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -400,7 +400,7 @@ Fields relating to the NIRS optode positions:
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -413,7 +413,7 @@ Fields relating to the position of fiducials measured during an NIRS session/run
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at
@@ -426,7 +426,7 @@ Fields relating to the position of anatomical landmarks measured during an NIRS
 
 <!-- This block generates a metadata table.
 These tables are defined in
-  src/schema/rules/sidecars
+  src/schema/rules/json
 The definitions of the fields specified in these tables may be found in
   src/schema/objects/metadata.yaml
 A guide for using macros can be found at

src/schema/README.md

@@ -873,9 +873,9 @@ meg_meg_common:
     description: optional
 ```
 
-### Sidecar and tabular data rules
+### JSON and tabular data rules
 
-Tabular data and JSON sidecar files follow a similar pattern:
+Tabular data and JSON files follow a similar pattern:
 
 |      | Name          | Value         |
 | ---- | ------------- | ------------- |
@@ -937,7 +937,7 @@ rule is applied.
 
 #### Valid fields for definitions
 
-1.  `rules.sidecars.*`
+1.  `rules.sidecars.*` and `rules.json.*`
 
     | Field       | Description                                                                                              |
     | ----------- | -------------------------------------------------------------------------------------------------------- |
@@ -984,6 +984,11 @@ MRIFuncVolumeTiming:
 An additional check will be required to assert that both are not present,
 but these tables may be combined for rendering purposes.
 
+`rules.json.*` and `rules.sidecars.*` are essentially identical,
+except `rules.json` rules describe the contents of individual JSON files,
+while `rules.sidecars` rules describe the contents of sidecar files,
+accumulated by the inheritance principle.
+
 Here we present an example rule in `rules.tabular_data.eeg`:
 
 ```YAML
@@ -1058,9 +1063,6 @@ EventsMissing:
     | ----------- | ------------------------------------- |
     | `datatypes` | List of datatypes mapping to modality |
 
--   `rules.dataset_metadata` - These are similar to `rules.sidecars.*`, for JSON files at the root level.
-    This is likely to go away in favor of other approaches.
-
 -   `rules.errors` - This file describes errors that cannot be expressed in the schema. This provides common
     codes and language that implementing validators can use to ensure the same problems are reported to
     users in the same way.

src/schema/SCHEMA_VERSION

@@ -1 +1 @@
-1.3.0-dev
+2.0.0-dev

src/schema/rules/json/atlas.yaml

@@ -0,0 +1,19 @@
+---
+atlas_description:
+  selectors:
+    - suffix == 'description'
+    - extension == '.json'
+    - entities.atlas
+  fields:
+    AtlasName: required
+    License: required
+    Description: recommended
+    Authors: recommended
+    Curators: optional
+    Funding: optional
+    ReferencesAndLinks: optional
+    Species: optional
+    AtlasSampleSize: optional
+    DerivedFrom: optional
+    LevelType: optional
+    RRID: optional

src/schema/rules/dataset_metadata.yaml → src/schema/rules/json/dataset.yaml

@@ -44,40 +44,3 @@ derivative_description:
     - json.DatasetType == "derivative"
   fields:
     GeneratedBy: required
-
-dataset_description_with_genetics:
-  selectors:
-    - path == "/dataset_description.json"
-    - exists('genetic_info.json', 'dataset')
-  fields:
-    Genetics: required
-
-genetic_info:
-  selectors:
-    - path == "/genetic_info.json"
-  fields:
-    GeneticLevel: required
-    SampleOrigin: required
-    AnalyticalApproach: optional
-    TissueOrigin: optional
-    BrainLocation: optional
-    CellType: optional
-
-atlas_description:
-  selectors:
-    - suffix == 'description'
-    - extension == '.json'
-    - entities.atlas
-  fields:
-    AtlasName: required
-    License: required
-    Description: recommended
-    Authors: recommended
-    Curators: optional
-    Funding: optional
-    ReferencesAndLinks: optional
-    Species: optional
-    AtlasSampleSize: optional
-    DerivedFrom: optional
-    LevelType: optional
-    RRID: optional

src/schema/rules/json/genetics.yaml

@@ -0,0 +1,18 @@
+---
+genetic_info:
+  selectors:
+    - path == "/genetic_info.json"
+  fields:
+    GeneticLevel: required
+    SampleOrigin: required
+    AnalyticalApproach: optional
+    TissueOrigin: optional
+    BrainLocation: optional
+    CellType: optional
+
+dataset_description_with_genetics:
+  selectors:
+    - path == "/dataset_description.json"
+    - exists('genetic_info.json', 'dataset')
+  fields:
+    Genetics: required

tools/schemacode/pyproject.toml

@@ -115,7 +115,7 @@ exclude_also = [
 # uvx bump-my-version bump <patch|minor|major>
 # git push upstream <current-branch>
 [tool.bumpversion]
-current_version = "1.3.0-dev"
+current_version = "2.0.0-dev"
 parse = """(?x)
     (?P<major>[0-9]+)
     \\.(?P<minor>[0-9]+)

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

@@ -57,7 +57,7 @@ def test_selectors(schema_obj):
     # For directories of files, need to look three down
     for rules, level in (
         (schema_obj.rules.checks, 3),
-        (schema_obj.rules.dataset_metadata, 2),
+        (schema_obj.rules.json, 3),
         (schema_obj.rules.sidecars, 3),
         (schema_obj.rules.tabular_data, 3),
         (schema_obj.rules.errors, 2),