#!/usr/bin/env python """schemas_a.py — batch A: identity chain (8 schemas). genome_ref, input_snapshot, host_profile, condition_card, evidence_item, circuit_design, kinetic_crn_ref, integration_candidate """ from schema_helpers import arr, aref, check, dec, obj, sha, schema, sref, ts_ SCHEMAS = {} SCHEMAS["genome_ref"] = schema( "genome_ref", "genome_ref@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "files", "contigs", "coord_convention", "source"], "properties": { "artifact_type": {"const": "genome_ref@1"}, "files": arr("seq", obj( { "path": {"type": "string", "minLength": 1, "maxLength": 1024}, "sha256": sha(), "format": {"enum": ["fasta", "genbank", "gff3", "other"]}, }, ["path", "sha256", "format"], )), "assembly": {"type": "string", "maxLength": 256}, "strain": {"type": "string", "maxLength": 256}, "taxon": {"type": "string", "maxLength": 256}, "contigs": arr("seq", obj( { "name": {"type": "string", "minLength": 1, "maxLength": 512}, "length": {"type": "integer", "minimum": 0}, "topology": {"enum": ["linear", "circular"]}, }, ["name", "length", "topology"], )), "coord_convention": {"enum": ["0-based-half-open", "1-based-inclusive"]}, "source": {"type": "string", "minLength": 1, "maxLength": 512}, "fetched_at": ts_(), }, }, ) SCHEMAS["input_snapshot"] = schema( "input_snapshot", "input_snapshot@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "role", "media_type", "format", "consumer_compatibility", "sha256", "byte_size", "origin"], "properties": { "artifact_type": {"const": "input_snapshot@1"}, "role": {"enum": [ "genome_sequence", "genome_annotation", "condition", "parts_evidence", "sbol", "cassette", "gem_model", "gem_card", "coupling_assumption", "other", ]}, "media_type": {"type": "string", "minLength": 1, "maxLength": 128}, "format": {"enum": ["fasta", "gff3", "genbank", "sbml", "json", "zip", "text", "other"]}, "consumer_compatibility": arr("set", {"type": "string", "minLength": 1, "maxLength": 64}), "sha256": sha(), "byte_size": {"type": "integer", "minimum": 0}, "origin": obj( { "kind": {"enum": ["external", "ingest_produced"]}, "origin_ref": {"type": "string", "maxLength": 512}, }, ["kind"], ), }, }, ) SCHEMAS["host_profile"] = schema( "host_profile", "host_profile@1 (host-side evidence state; no product tier)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "genome_ref", "evidence_state", "derived", "gates"], "properties": { "artifact_type": {"const": "host_profile@1"}, "genome_ref": aref(), "evidence_state": obj( { "annotation": obj( {"completeness": {"enum": ["full", "partial", "missing"]}, "detail": {"type": "string", "maxLength": 2048}}, ["completeness"], ), "condition": obj( {"completeness": {"enum": ["full", "partial", "missing"]}, "detail": {"type": "string", "maxLength": 2048}}, ["completeness"], ), "parts_evidence": obj( { "completeness": {"enum": ["full", "partial", "missing"]}, "source_id": {"type": "string", "maxLength": 256}, "hash": sha(), "levels": arr("set", {"enum": ["E0", "E1", "E2", "E3"]}), "detail": {"type": "string", "maxLength": 2048}, }, ["completeness"], ), }, ["annotation", "condition", "parts_evidence"], ), "derived": obj( { "genome_size": {"type": "integer", "minimum": 0}, "gc_percent": {"type": "number", "minimum": 0, "maximum": 100}, "contig_count": {"type": "integer", "minimum": 0}, "codon_usage_top": arr("seq", obj( { "codon": {"type": "string", "minLength": 3, "maxLength": 3}, "fraction": {"type": "number", "minimum": 0, "maximum": 1}, }, ["codon", "fraction"], )), }, ["genome_size", "gc_percent", "contig_count"], ), "condition_ref": aref(), "gates": arr("set", check()), }, }, ) SCHEMAS["condition_card"] = schema( "condition_card", "condition_card@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "medium", "culture_mode", "readout"], "properties": { "artifact_type": {"const": "condition_card@1"}, "medium": obj( { "name": {"type": "string", "maxLength": 256}, "carbon_sources": arr("set", {"type": "string", "minLength": 1, "maxLength": 128}), "uptake_definition": {"type": "string", "maxLength": 2048}, "oxygen": {"enum": ["aerobic", "microaerobic", "anaerobic", "unspecified"]}, "temperature_c": {"type": "number", "minimum": 0, "maximum": 120}, "ph": {"type": "number", "minimum": 0, "maximum": 14}, }, ["carbon_sources", "oxygen"], ), "culture_mode": {"enum": ["batch", "fed_batch", "continuous", "unspecified"]}, "copy_number": obj( { "value": {"type": "integer", "minimum": 0}, "integration_status": {"enum": ["integrated", "plasmid", "unspecified"]}, }, ["integration_status"], ), "readout": obj( { "kind": {"type": "string", "minLength": 1, "maxLength": 256}, "unit": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["kind", "unit"], ), }, }, ) SCHEMAS["evidence_item"] = schema( "evidence_item", "evidence_item@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "source_ref", "host", "readout", "match_grade", "matching_policy"], "properties": { "artifact_type": {"const": "evidence_item@1"}, "source_ref": obj( { "kind": {"enum": ["doi", "pmid", "url", "lab", "other"]}, "id": {"type": "string", "minLength": 1, "maxLength": 512}, }, ["kind", "id"], ), "source_hash": sha(), "host": obj( { "organism": {"type": "string", "minLength": 1, "maxLength": 256}, "strain": {"type": "string", "maxLength": 256}, "assembly": {"type": "string", "maxLength": 256}, }, ["organism"], ), "conditions": obj( { "medium": {"type": "string", "maxLength": 256}, "temperature_c": {"type": "number", "minimum": 0, "maximum": 120}, "ph": {"type": "number", "minimum": 0, "maximum": 14}, }, [], ), "part_sequence": obj( { "name": {"type": "string", "minLength": 1, "maxLength": 256}, "sequence": {"type": "string", "minLength": 1, "maxLength": 100000}, }, ["name", "sequence"], ), "readout": obj( { "metric": {"type": "string", "minLength": 1, "maxLength": 256}, "value": dec(), "unit": {"type": "string", "minLength": 1, "maxLength": 64}, "replicates": {"type": "integer", "minimum": 1}, }, ["metric", "value", "unit", "replicates"], ), "match_grade": {"enum": ["exact", "condition_transfer", "host_transfer", "unknown"]}, "matching_policy": obj( { "id": {"type": "string", "minLength": 1, "maxLength": 128}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["id", "version"], ), }, }, ) SCHEMAS["circuit_design"] = schema( "circuit_design", "circuit_design@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "source", "template_ref"], "properties": { "artifact_type": {"const": "circuit_design@1"}, "source": {"enum": ["sbol_file", "components"]}, "components": arr("seq", obj( { "part_id": {"type": "string", "maxLength": 256}, "kind": {"enum": ["promoter", "rbs", "cds", "terminator", "spacer", "other"]}, "sequence": {"type": "string", "minLength": 1, "maxLength": 100000}, }, ["kind"], )), "sequence_hashes": arr("set", sha()), "orientation": {"enum": ["forward", "reverse", "unspecified"]}, "constraints": arr("set", {"type": "string", "minLength": 1, "maxLength": 512}), "part_refs": arr("set", obj( { "part_id": {"type": "string", "minLength": 1, "maxLength": 256}, "evidence_level": {"enum": ["E0", "E1", "E2", "E3"]}, }, ["part_id", "evidence_level"], )), "template_ref": obj( { "template_id": {"enum": ["expression_balance", "metabolic_valve"]}, "version": {"type": "string", "minLength": 1, "maxLength": 64}, }, ["template_id", "version"], ), "parameters": {"type": "object", "additionalProperties": True}, "conformance": obj( { "status": {"enum": ["pass", "fail", "not_run"]}, "detail": {"type": "string", "maxLength": 2048}, }, ["status"], ), }, }, ) SCHEMAS["kinetic_crn_ref"] = schema( "kinetic_crn_ref", "kinetic_crn_ref@1", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "model_kind", "sbml_ref"], "properties": { "artifact_type": {"const": "kinetic_crn_ref@1"}, "model_kind": {"const": "kinetic_crn"}, "sbml_ref": aref(), "compiled_from": obj( { "source": {"type": "string", "maxLength": 512}, "tool": {"type": "string", "maxLength": 128}, }, ["source", "tool"], ), }, }, ) SCHEMAS["integration_candidate"] = schema( "integration_candidate", "integration_candidate@1 (never emits a safety claim)", { "type": "object", "additionalProperties": False, "required": ["artifact_type", "genome_ref", "ruleset_ref", "contig", "interval", "strand", "cassette", "classification", "screening_stage", "reasons", "counts"], "properties": { "artifact_type": {"const": "integration_candidate@1"}, "genome_ref": aref(), "ruleset_ref": aref(), "contig": {"type": "string", "minLength": 1, "maxLength": 512}, "interval": obj( { "start": {"type": "integer", "minimum": 0}, "end": {"type": "integer", "minimum": 0}, "convention": {"const": "0-based-half-open"}, }, ["start", "end", "convention"], ), "strand": {"enum": ["plus", "minus"]}, "cassette": obj( { "sequence_sha256": sha(), "payload_length": {"type": "integer", "minimum": 0}, "sequence_identity": {"enum": ["known", "unknown"]}, }, ["sequence_identity"], ), "classification": {"enum": ["excluded", "preliminary_candidate", "screened_candidate", "literature_characterized", "blocked"]}, "screening_stage": {"enum": ["preliminary_spatial", "sequence_verified"]}, "reasons": arr("set", obj( { "rule_id": {"type": "string", "minLength": 1, "maxLength": 128}, "code": {"type": "string", "maxLength": 128}, "detail": {"type": "string", "maxLength": 2048}, }, ["rule_id"], )), "features_hit": arr("set", {"type": "string", "minLength": 1, "maxLength": 256}), "flanking": obj( { "left": obj({"start": {"type": "integer", "minimum": 0}, "end": {"type": "integer", "minimum": 0}}, ["start", "end"]), "right": obj({"start": {"type": "integer", "minimum": 0}, "end": {"type": "integer", "minimum": 0}}, ["start", "end"]), }, ["left", "right"], ), "origin_crossing": {"type": "boolean"}, "normalized_flank_hashes": obj( {"left": sha(), "right": sha()}, ["left", "right"], ), "counts": obj( { "searched_space": {"type": "integer", "minimum": 0}, "excluded": {"type": "integer", "minimum": 0}, "unknown": {"type": "integer", "minimum": 0}, "mandatory_rule_coverage": arr("set", obj( { "rule_id": {"type": "string", "minLength": 1, "maxLength": 128}, "covered": {"type": "integer", "minimum": 0}, }, ["rule_id", "covered"], )), }, ["searched_space", "excluded", "unknown", "mandatory_rule_coverage"], ), }, }, )