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Covers class hierarchy design, validation continuity, Python/TypeScript code generation, and CI integration. Scoped to metaschema replacement only — the BIDS schema YAML files are not modified. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add bids_metaschema.yaml with: - RequirementLevel enum (required/recommended/optional/deprecated) - FormatType enum (17 format identifiers matching current metaschema) - IssueSeverity enum (error/warning) - GeneralTerm base class (display_name, description) Also add linkml_design_steps.md with detailed Phase 1 substeps. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add class hierarchy for all BIDS schema object types: - ValueTerm -> Datatype, Extension, Suffix, EnumValue - NameValueTerm -> Entity, MetadataField, Column - Format, FileObject (independent GeneralTerm subclasses) - PrivateEnum (underscore-prefixed enum definitions) - JsonSchema (loosely-typed container for embedded JSON Schema) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add rule classes: - SuffixRule, PathRule, StemRule (file naming rules) - SidecarRule (JSON sidecar field rules) - TabularDataRule (TSV column rules) - CheckRule (validation check rules) - FieldSpec, EntityOverride (rule sub-components) - Issue, ErrorDefinition (validation messages) - ModalityMapping, DirectoryEntry (supporting types) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add meta classes: - Association + AssociationTarget (file association rules) - ExpressionTest (expression language test cases) - Template (reusable partial rule fragments) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add container classes completing the schema structure: - BidsSchema (tree_root): meta, objects, rules, versions - MetaSection: associations, context, expression_tests, templates - ObjectsSection: all 12 object sub-namespace maps - RulesSection: checks, files, sidecars, tabular_data, etc. - FileRulesSection: common/raw/deriv file rule groups Total: 38 LinkML class and enum definitions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add patch_metaschema.py to post-process LinkML-generated JSON Schema, adding map types (additionalProperties) that LinkML cannot express natively. Fix Template to allow suffixes/extensions fields. The pipeline: gen-json-schema | patch_metaschema.py produces a JSON Schema that successfully validates the compiled BIDS schema, achieving parity with the existing src/metaschema.json. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Categorize all 43 JSON Schema patches into 6 groups and analyze how LinkML's extra_slots feature (not yet implemented in gen-json-schema) could eliminate most of them once it ships. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Using the draft extra_slots implementation from sneakers-the-rat/linkml@jsonschema-extra (linkml/linkml#2940), replace 35 of 43 post-processing patches with native LinkML declarations: - Category 4 (8 patches): extra_slots: {allowed: true} on open classes (MetadataField, Column, Suffix, etc.) - Category 1 (16 patches): 13 typed map wrapper classes with extra_slots: {range_expression: {range: X}} - Category 2 (9 patches): 12 nested map wrapper classes (CheckRuleGroupMap -> CheckRuleMap -> CheckRule, etc.) - Category 3 (4 patches): 3 union map classes with any_of in range_expression (EntityRequirementMap, FieldRequirementMap, etc.) Remaining 8 patches: 5 slot-level type coercions, 2 sidecars/ tabular_data derivatives nesting overrides, 1 root $ref. Key divergence in PR 2940: extra_slots generates spurious {type: null} in additionalProperties anyOf for class-ranged maps. This does not break validation but is less strict than intended. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…data dir - Create gen_class_diagram.py: generates Mermaid classDiagram from bids_metaschema.yaml showing 35 data model classes, 3 enums, inheritance and composition relationships (excludes 29 map wrappers) - Create class_diagram.md: auto-generated Mermaid diagram output - Update linkml_design_plan.md: add Class Hierarchy Diagram section - Move bids_metaschema.yaml from src/schema/ to src/ to prevent _read_yaml_dir from loading it as schema data (broke load_schema) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
while we reviewed rendering of classes diagram
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Ongoing work with @effigies and claude code.