#!/usr/bin/env python """schemas_c.py — batch C: policy/governance + embed/audit/container (7 schemas). numeric_policy, unit_vocabulary, integration_ruleset, provenance_dag, claim, tool_result, case_manifest """ from schema_helpers import arr, aref, check, dec, obj, sha, schema, sref, ts_ SCHEMAS = {} SCHEMAS["numeric_policy"] = schema( "numeric_policy", "numeric_policy@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "fva_fraction_of_optimum", "solver", "tolerance", "direction_epsilon", "near_zero_rule", "interval_zero_crossing_rule"], "properties": { "artifact_type": {"const": "numeric_policy@1"}, "fva_fraction_of_optimum": {"type": "number", "minimum": 0, "maximum": 1}, "solver": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 64}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "version"], ), "tolerance": {"type": "number", "exclusiveMinimum": 0}, "direction_epsilon": dec(), "near_zero_rule": {"type": "string", "minLength": 1, "maxLength": 1024}, "interval_zero_crossing_rule": {"enum": ["crossing_flags_indeterminate", "crossing_allowed_with_note"]}, }, }, ) SCHEMAS["unit_vocabulary"] = schema( "unit_vocabulary", "unit_vocabulary@1 (units + dimension algebra + forbidden mixes)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "units", "conversions", "forbidden_mixes"], "properties": { "artifact_type": {"const": "unit_vocabulary@1"}, "units": arr("set", obj( { "unit_id": {"type": "string", "minLength": 1, "maxLength": 64}, "symbol": {"type": "string", "minLength": 1, "maxLength": 32}, "dimension": arr("set", obj( { "base": {"enum": ["mass", "length", "time", "amount", "charge", "temperature", "dimensionless"]}, "exponent": {"type": "integer"}, }, ["base", "exponent"], )), }, ["unit_id", "symbol", "dimension"], )), "conversions": arr("set", obj( { "from": {"type": "string", "minLength": 1, "maxLength": 64}, "to": {"type": "string", "minLength": 1, "maxLength": 64}, "factor": dec(), "note": {"type": "string", "maxLength": 1024}, }, ["from", "to", "factor"], )), "forbidden_mixes": arr("set", obj( { "a": {"type": "string", "minLength": 1, "maxLength": 64}, "b": {"type": "string", "minLength": 1, "maxLength": 64}, "reason": {"type": "string", "minLength": 1, "maxLength": 1024}, }, ["a", "b", "reason"], )), }, }, ) SCHEMAS["integration_ruleset"] = schema( "integration_ruleset", "integration_ruleset@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "ruleset_id", "version", "rules"], "properties": { "artifact_type": {"const": "integration_ruleset@1"}, "ruleset_id": {"type": "string", "minLength": 1, "maxLength": 128}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, "rules": arr("set", obj( { "rule_id": {"type": "string", "minLength": 1, "maxLength": 128}, "kind": {"enum": ["feature_overlap", "repeat", "essentiality", "neighborhood", "motif", "other"]}, "mandatory": {"type": "boolean"}, "params": {"type": "object", "additionalProperties": True}, "description": {"type": "string", "maxLength": 1024}, }, ["rule_id", "kind", "mandatory"], )), }, }, ) SCHEMAS["provenance_dag"] = schema( "provenance_dag", "provenance_dag@1 (nodes artifact/claim; typed edges; canonical sort + DAG hash)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "nodes", "edges", "dag_hash"], "properties": { "artifact_type": {"const": "provenance_dag@1"}, "nodes": arr("set", obj( { "id": sha(), "kind": {"enum": ["artifact", "claim"]}, "type": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "kind", "type"], )), "edges": arr("set", obj( { "from": sha(), "to": sha(), "kind": {"enum": ["consumes", "derives_from", "supports", "assumes"]}, }, ["from", "to", "kind"], )), "dag_hash": sha(), }, }, ) SCHEMAS["claim"] = schema( "claim", "claim@1 (embed-only; classification gates mandatory fields)", { "type": "object", "additionalProperties": False, "required": ["claim_id", "classification", "status"], "properties": { "claim_id": sha(), "classification": {"enum": ["FACT", "ASSUMPTION", "INFERENCE", "BLOCKED"]}, "status": {"enum": ["SUPPORTED", "CONDITIONAL", "INDETERMINATE", "BLOCKED"]}, "evidence_refs": arr("set", sha()), "assumption_refs": arr("set", sha()), "method_ref": {"type": "string", "maxLength": 512}, "domain_ref": {"type": "string", "maxLength": 512}, "uncertainty": {"type": "string", "maxLength": 2048}, "limitations": arr("set", {"type": "string", "minLength": 1, "maxLength": 2048}), }, "allOf": [ { "if": {"type": "object", "properties": {"classification": {"const": "FACT"}}}, "then": { "type": "object", "required": ["evidence_refs"], "properties": {"evidence_refs": {"type": "array", "minItems": 1}}, }, }, { "if": {"type": "object", "properties": {"classification": {"const": "ASSUMPTION"}}}, "then": { "type": "object", "required": ["assumption_refs"], "properties": {"assumption_refs": {"type": "array", "minItems": 1}}, }, }, { "if": {"type": "object", "properties": {"classification": {"const": "INFERENCE"}}}, "then": { "type": "object", "required": ["method_ref", "domain_ref", "uncertainty"], "properties": { "method_ref": {"type": "string"}, "domain_ref": {"type": "string"}, "uncertainty": {"type": "string"}, }, }, }, ], }, ) SCHEMAS["tool_result"] = schema( "tool_result", "tool_result@1 (audit-only; never a scientific input)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "audit_only", "status", "generated_by"], "properties": { "artifact_type": {"const": "tool_result@1"}, "audit_only": {"const": True}, "status": {"enum": ["OK", "BLOCKED", "NOT_RUN", "OUT_OF_DOMAIN", "DEPENDENCY_UNAVAILABLE", "INVALID_INPUT", "EXECUTION_ERROR"]}, "reason_code": {"type": "string", "minLength": 1, "maxLength": 128}, "reason_codes": arr("set", {"type": "string", "minLength": 1, "maxLength": 128}), "artifact_refs": arr("set", aref()), "detail": {"type": "string", "maxLength": 8192}, "input_hashes": arr("set", sha()), "producer": {"type": "string", "maxLength": 256}, "generated_by": {"enum": ["ts_wrapper", "python_worker"]}, "stderr_summary": {"type": "string", "maxLength": 4096}, }, }, ) SCHEMAS["case_manifest"] = schema( "case_manifest", "case_manifest@1 (canonical snapshot manifest; snapshot_sha = sha256(canonical(doc without snapshot_sha)))", { "type": "object", "additionalProperties": False, "required": ["schema_version", "case_content_id", "artifacts", "policy"], "properties": { "schema_version": {"const": "1.0"}, "case_content_id": sha(), "snapshot_sha": sha(), "artifacts": arr("set", obj( { "artifact_id": sha(), "type": {"enum": [ "genome_ref@1", "input_snapshot@1", "host_profile@1", "condition_card@1", "evidence_item@1", "circuit_design@1", "kinetic_crn_ref@1", "integration_candidate@1", "expression_scenario@1", "gem_card_raw@1", "metabolic_model_ref@1", "host_model_binding@1", "gpr_proof@1", "coupling_profile@1", "consequence_run@1", "tier_decision@1", "numeric_policy@1", "unit_vocabulary@1", "integration_ruleset@1", "provenance_dag@1", "case_report@1", ]}, "inputs": arr("set", sha()), "producer": {"type": "string", "minLength": 1, "maxLength": 256}, "schema_major": {"const": "1"}, "canonical_path": {"type": "string", "minLength": 1, "maxLength": 1024}, }, ["artifact_id", "type", "inputs", "producer", "schema_major", "canonical_path"], )), "policy": obj( { "policy_id": {"type": "string", "minLength": 1, "maxLength": 128}, "policy_version": {"type": "string", "minLength": 1, "maxLength": 64}, "policy_hash": sha(), }, ["policy_id", "policy_version", "policy_hash"], ), }, }, )