Add minischema/profile mechanism and new field types (ontology, quantity, relative_quantity)#13
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Replace the per-kind treatment schemas (treatment_drug, virus_injection) with a single generic treatment document whose manipulation field's shape is delegated to a named profile (minischema). This removes schema-file proliferation for the treatment family while preserving rigor via ontology-anchored profiles and keeping search tractable via canonical units, promoted fields, and profile_id references. Meta-schema changes: - Add ontology, quantity, relative_quantity to the type enum. - Add _shape_from_minischema (boolean) on structure fields; when true, the nested _fields is not required. New: profile_meta.json validates profile files; type-specific _constraints rules (canonical_unit + canonical_unit_label on quantity; add reference on relative_quantity; descendant_of permitted on ontology). New: schemas/V_beta/profiles/virus_injection.json canonical profile. treatment.json rewritten as a generic document with a single manipulation field that delegates its shape via _shape_from_minischema. Version bumped to 2.0.0. Retired: treatment_drug.json, virus_injection.json. stimulus_bath intentionally retained (it's a stimulus approach, not a treatment). Tests: tests/test_minischema.py covers new types, _shape_from_minischema conditional, profile validation, canonical profile contents, and regression over all existing V_beta schemas against the updated meta-schema. 28 new tests, all passing. Follow-on work (drug_treatment profile, mammalian stereotaxic profile, cross-profile canonical-unit registry) captured in Ideas.md.
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Summary
This PR introduces a new minischema (profile) mechanism for V_beta schemas, enabling reusable schema fragments that define the shape of structure fields at runtime. It also adds three new field types (
ontology,quantity,relative_quantity) to support richer semantic and measurement data. The treatment family is consolidated from three separate schemas into a single generictreatmentschema that delegates itsmanipulationfield shape to profiles.Key Changes
New meta-schema:
profile_meta.jsonvalidates profile (minischema) files with type-specific constraint rules:quantityfields requirecanonical_unitandcanonical_unit_labelrelative_quantityfields additionally require areferenceanchorontologyfields forbidcanonical_unitUpdated meta-schema:
did_schema_meta.jsonnow:ontology,quantity,relative_quantity_shape_from_minischema: trueon structure fields to delegate shape to profiles_fieldspresence when shape is not delegatedNew canonical profile:
profiles/virus_injection.jsondemonstrates the profile mechanism with:Treatment consolidation:
treatment_drug.jsonandvirus_injection.jsonschemastreatment.jsonto use_shape_from_minischema: trueon themanipulationfieldtreatment._class_versionto 2.0.0 (breaking change)base/schema.jsontobase.jsonComprehensive test suite:
tests/test_minischema.pyvalidates:Documentation updates:
V_beta_SPEC.mdandV_beta_notes.mddocument the new types, profile mechanism, and consolidation rationaleImplementation Details
schemas/V_beta/profiles/with their own versioning and maturity levels_shape_from_minischemaflag allows structure fields to omit inline_fieldswhen shape is supplied at runtime via a document's_minischemakeycanonical_unit_label) plussource_valueandsource_unitfor provenanceextendsfield enables profile composition (e.g., organism-specific or route-specific virus injection profiles)https://claude.ai/code/session_011acLkncHaNtT8YnEeVjWAA