#!/usr/bin/env python """schemas_b.py — batch B: analysis chain (8 schemas). expression_scenario, gem_card_raw, metabolic_model_ref, host_model_binding, gpr_proof, coupling_profile, consequence_run, tier_decision """ from schema_helpers import arr, aref, check, dec, obj, sha, schema, sref, ts_ SCHEMAS = {} SCHEMAS["expression_scenario"] = schema( "expression_scenario", "expression_scenario@1 (no absolute-expression claims outside domain)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "circuit_design", "host_profile", "method", "results", "domain_check", "ranking_set_id", "comparison_scope", "metric_definition", "higher_is"], "properties": { "artifact_type": {"const": "expression_scenario@1"}, "circuit_design": aref(), "host_profile": aref(), "method": {"enum": ["evidence_lookup", "ostir_proxy", "user_parameters"]}, "results": arr("set", obj( { "element": {"type": "string", "minLength": 1, "maxLength": 256}, "metric": {"type": "string", "minLength": 1, "maxLength": 256}, "value_or_rank": obj( { "kind": {"enum": ["value", "rank"]}, "value": dec(), "rank": {"type": "integer", "minimum": 1}, }, ["kind"], ), "unit": {"type": "string", "maxLength": 64}, "conditions": {"type": "string", "maxLength": 256}, "evidence_level": {"enum": ["E0", "E1", "E2", "E3"]}, }, ["element", "metric", "value_or_rank"], )), "domain_check": {"enum": ["in_domain", "out_of_domain", "unknown"]}, "assumptions": arr("set", {"type": "string", "minLength": 1, "maxLength": 2048}), "ranking_set_id": {"type": "string", "minLength": 1, "maxLength": 128}, "comparison_scope": {"type": "string", "minLength": 1, "maxLength": 256}, "metric_definition": {"type": "string", "minLength": 1, "maxLength": 512}, "higher_is": {"enum": ["high", "low"]}, "sequence_context_ref": aref(), "model_or_dataset_ref": aref(), "parameter_hash": sha(), "uncertainty": {"type": "string", "maxLength": 2048}, "candidate_universe_ref": aref(), "rank_algorithm": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 128}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, "params": {"type": "object", "additionalProperties": True}, }, ["id", "version"], ), "tie_null_policy": {"type": "string", "maxLength": 512}, "raw_metric_artifact_ref": aref(), "filter_records": arr("set", obj( { "filter_id": {"type": "string", "minLength": 1, "maxLength": 128}, "detail": {"type": "string", "maxLength": 1024}, }, ["filter_id"], )), }, }, ) SCHEMAS["gem_card_raw"] = schema( "gem_card_raw", "gem_card_raw@1 (frozen raw card bytes; no runtime augmentation)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "card_schema", "raw_sha256", "raw_bytes_ref"], "properties": { "artifact_type": {"const": "gem_card_raw@1"}, "card_schema": {"enum": ["v2", "v3", "legacy_missing_schema", "unsupported_major"]}, "raw_sha256": sha(), "raw_bytes_ref": aref(), "original_filename": {"type": "string", "maxLength": 512}, }, }, ) SCHEMAS["metabolic_model_ref"] = schema( "metabolic_model_ref", "metabolic_model_ref@1 (regenerated by Genie; independent of gem card open fields)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "sbml_ref", "card", "model_id", "genome_link", "gpr", "objective", "baseline"], "properties": { "artifact_type": {"const": "metabolic_model_ref@1"}, "sbml_ref": aref(), "card": obj( { "card_schema": {"enum": ["v2", "v3", "legacy_missing_schema", "unsupported_major"]}, "card_ref": aref(), }, ["card_schema"], ), "model_id": {"type": "string", "minLength": 1, "maxLength": 256}, "genome_link": obj( { "assembly": {"type": "string", "maxLength": 256}, "strain": {"type": "string", "maxLength": 256}, "genome_sha256": sha(), "match_status": {"enum": ["exact", "evidence_missing", "conflict", "unresolved"]}, }, ["match_status"], ), "gpr": obj( { "coverage_pct": {"type": "number", "minimum": 0, "maximum": 100}, "namespace": {"type": "string", "minLength": 1, "maxLength": 128}, "crosswalk_status": {"enum": ["exact", "versioned_alias", "ambiguous", "unmapped"]}, }, ["coverage_pct", "namespace", "crosswalk_status"], ), "medium_ref": aref(), "objective": {"type": "string", "minLength": 1, "maxLength": 256}, "validation_claim": {"type": "string", "maxLength": 4096}, "baseline": obj( { "feasible": {"type": "boolean"}, "growth": dec(), "solver": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 64}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "version"], ), }, ["feasible", "solver"], ), }, }, ) SCHEMAS["host_model_binding"] = schema( "host_model_binding", "host_model_binding@1 (only exact enters reference quantitative use)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "genome_sha256", "model_sbml_sha256", "binding_method", "evidence_source", "match_result"], "properties": { "artifact_type": {"const": "host_model_binding@1"}, "genome_sha256": sha(), "model_sbml_sha256": sha(), "binding_method": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 128}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "version"], ), "evidence_source": {"type": "string", "minLength": 1, "maxLength": 1024}, "match_result": {"enum": ["exact", "evidence_missing", "conflict", "unresolved"]}, }, }, ) SCHEMAS["gpr_proof"] = schema( "gpr_proof", "gpr_proof@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "canonical_gpr_ast", "ast_hash", "source_gene_ids", "gem_gene_ids", "namespace", "reaction_id", "mapping_path"], "properties": { "artifact_type": {"const": "gpr_proof@1"}, "canonical_gpr_ast": {"type": "string", "minLength": 1, "maxLength": 65536}, "ast_hash": sha(), "source_gene_ids": arr("set", {"type": "string", "minLength": 1, "maxLength": 256}), "gem_gene_ids": arr("set", {"type": "string", "minLength": 1, "maxLength": 256}), "namespace": {"type": "string", "minLength": 1, "maxLength": 128}, "reaction_id": {"type": "string", "minLength": 1, "maxLength": 256}, "mapping_path": arr("seq", {"type": "string", "minLength": 1, "maxLength": 512}), }, }, ) _RULE = { "type": "object", "additionalProperties": False, "required": ["rule_id", "model_ref", "host_profile", "host_model_binding_ref", "gpr_proof_ref", "condition_card_ref", "source_gene", "reaction_id", "reaction_direction", "operation", "baseline_bound", "derived_bound", "unit", "mapping_function", "condition_hash", "input_kind", "evidence_refs", "assumption_refs", "confidence"], "properties": { "rule_id": {"type": "string", "minLength": 1, "maxLength": 128}, "model_ref": aref(), "host_profile": aref(), "host_model_binding_ref": aref(), "gpr_proof_ref": aref(), "condition_card_ref": aref(), "source_gene": obj( { "namespace": {"type": "string", "minLength": 1, "maxLength": 128}, "id": {"type": "string", "minLength": 1, "maxLength": 256}, }, ["namespace", "id"], ), "reaction_id": {"type": "string", "minLength": 1, "maxLength": 256}, "reaction_direction": {"enum": ["forward", "reverse", "both"]}, "operation": {"enum": ["set_upper_bound", "set_lower_bound", "scale_bound"]}, "baseline_bound": dec(), "derived_bound": dec(), "unit": {"type": "string", "minLength": 1, "maxLength": 64}, "mapping_function": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 128}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, "parameters": {"type": "object", "additionalProperties": True}, }, ["id", "version", "parameters"], ), "condition_hash": sha(), "input_kind": {"enum": ["user_explicit_assumption", "measured_expression", "literature_calibration", "sequence_proxy", "manual_override"]}, "evidence_refs": arr("set", sha()), "assumption_refs": arr("set", sha()), "confidence": {"enum": ["high", "medium", "low"]}, }, "allOf": [ { "if": {"type": "object", "properties": {"input_kind": {"const": "manual_override"}}}, "then": { "type": "object", "required": ["assumption_refs"], "properties": {"assumption_refs": {"type": "array", "minItems": 1}}, }, }, ], } SCHEMAS["coupling_profile"] = schema( "coupling_profile", "coupling_profile@1 (the only authorized cross-layer entry)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "mode", "rules"], "properties": { "artifact_type": {"const": "coupling_profile@1"}, "mode": {"enum": ["qualitative_direction", "user_calibrated_bound", "evidence_calibrated_bound"]}, "rules": arr("set", _RULE), "scope_check": obj( { "authorized": {"type": "boolean"}, "detail": {"type": "string", "maxLength": 2048}, }, ["authorized"], ), "blocked_reasons": arr("set", {"type": "string", "minLength": 1, "maxLength": 1024}), }, "allOf": [ { "if": {"type": "object", "properties": {"mode": {"const": "evidence_calibrated_bound"}}}, "then": { "type": "object", "properties": { "rules": { "type": "array", "items": { "type": "object", "properties": {"input_kind": {"not": {"const": "manual_override"}}}, }, }, }, }, }, { "if": {"type": "object", "properties": {"mode": {"not": {"const": "qualitative_direction"}}}}, "then": { "type": "object", "properties": { "rules": { "type": "array", "items": { "type": "object", "properties": {"input_kind": {"not": {"const": "sequence_proxy"}}}, }, }, }, }, }, { "if": {"type": "object", "properties": {"mode": {"not": {"const": "user_calibrated_bound"}}}}, "then": { "type": "object", "properties": { "rules": { "type": "array", "items": { "type": "object", "properties": {"input_kind": {"not": {"const": "manual_override"}}}, }, }, }, }, }, ], }, ) _SCENARIO = { "type": "object", "additionalProperties": False, "required": ["name", "diffs", "fba", "model_hash", "diff_hash", "medium_artifact_id", "applied_rule_ids", "mapping_proof_ids", "target_metric"], "properties": { "name": {"type": "string", "minLength": 1, "maxLength": 256}, "diffs": arr("set", obj( { "rule_id": {"type": "string", "minLength": 1, "maxLength": 128}, "reaction_id": {"type": "string", "minLength": 1, "maxLength": 256}, "old_value": dec(), "new_value": dec(), "unit": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["rule_id", "reaction_id", "old_value", "new_value", "unit"], )), "fba": obj( { "status": {"enum": ["optimal", "infeasible", "unbounded", "non_optimal", "timeout", "not_run"]}, "value": dec(), }, ["status"], ), "fva": obj( { "intervals": arr("set", obj( { "reaction_id": {"type": "string", "minLength": 1, "maxLength": 256}, "min": dec(), "max": dec(), }, ["reaction_id", "min", "max"], )), }, ["intervals"], ), "pfba": obj( { "status": {"enum": ["optimal", "infeasible", "unbounded", "non_optimal", "timeout", "not_run"]}, "value": dec(), }, ["status"], ), "model_hash": sha(), "diff_hash": sha(), "medium_artifact_id": sha(), "applied_rule_ids": arr("set", {"type": "string", "minLength": 1, "maxLength": 128}), "mapping_proof_ids": arr("set", sha()), "target_metric": {"type": "string", "minLength": 1, "maxLength": 256}, }, } SCHEMAS["consequence_run"] = schema( "consequence_run", "consequence_run@1 (direction is per claim_target; failed scenarios never yield ROBUST_DIRECTION)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "model_ref", "coupling_ref", "numeric_policy_ref", "medium_ref", "objective", "baseline", "scenarios", "claim_targets"], "properties": { "artifact_type": {"const": "consequence_run@1"}, "model_ref": aref(), "coupling_ref": aref(), "numeric_policy_ref": aref(), "medium_ref": aref(), "objective": {"type": "string", "minLength": 1, "maxLength": 256}, "baseline": obj( { "feasible": {"type": "boolean"}, "status": {"enum": ["optimal", "infeasible", "unbounded", "non_optimal", "timeout", "not_run"]}, "objective_value": dec(), "solver": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 64}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "version"], ), "options": {"type": "object", "additionalProperties": True}, }, ["feasible", "status", "solver"], ), "scenarios": arr("set", _SCENARIO), "claim_targets": arr("set", obj( { "kind": {"enum": ["growth", "product", "reaction"]}, "reaction_id": {"type": "string", "maxLength": 256}, "direction": {"enum": ["ROBUST_DIRECTION", "MIXED", "INDETERMINATE", "NOT_RUN"]}, "claim_id": sha(), }, ["kind", "direction"], )), "diagnostics": {"type": "string", "maxLength": 4096}, }, }, ) SCHEMAS["tier_decision"] = schema( "tier_decision", "tier_decision@1 (operation-level, recomputed from snapshot; input_snapshot_id points at the parent snapshot only)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "policy_id", "policy_version", "policy_hash", "input_snapshot_id", "per_operation"], "properties": { "artifact_type": {"const": "tier_decision@1"}, "policy_id": {"type": "string", "minLength": 1, "maxLength": 128}, "policy_version": {"type": "string", "minLength": 1, "maxLength": 64}, "policy_hash": sha(), "input_snapshot_id": sha(), "input_artifact_ids": arr("set", sha()), "per_operation": arr("set", obj( { "operation": {"type": "string", "minLength": 1, "maxLength": 64}, "max_tier": {"enum": ["reference_profile", "transfer_profile", "structural_only", "blocked"]}, "gates": arr("set", check()), "decision": {"enum": ["allow", "deny"]}, "capabilities": arr("set", {"type": "string", "minLength": 1, "maxLength": 64}), "reason_codes": arr("set", {"type": "string", "minLength": 1, "maxLength": 64}), }, ["operation", "max_tier", "gates", "decision", "capabilities", "reason_codes"], )), "gaps": arr("set", {"type": "string", "minLength": 1, "maxLength": 1024}), }, }, )