{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "ProgramDossier",
  "description": "Single state object threaded through all 10 stages of the drug-program pipeline. Read on stage entry, updated on stage exit. The source of truth for the program.",
  "type": "object",
  "required": ["schema_version", "disease", "created_at", "stages", "gates", "decisions", "open_questions"],
  "properties": {
    "schema_version": {"type": "string", "const": "1.0"},
    "disease": {"type": "string", "description": "Indication name as scoped by the user."},
    "scope": {
      "type": "object",
      "description": "Population/subtype/geography scope locked at Stage 1.",
      "properties": {
        "population": {"type": "string"},
        "subtype": {"type": "string"},
        "geography": {"type": "string"}
      }
    },
    "created_at": {"type": "string", "format": "date-time"},
    "updated_at": {"type": "string", "format": "date-time"},
    "disease_archetype": {
      "type": ["string", "null"],
      "description": "Genetic-architecture archetype, set at Stage 1b / ARCHETYPE LOCK. Reshapes Stages 3/4/5/8/9.",
      "enum": [null, "monogenic", "oligogenic", "polygenic_complex", "chromosomal", "mitochondrial", "somatic", "unknown"]
    },
    "mechanism_of_pathogenesis": {
      "type": ["string", "null"],
      "description": "For monogenic disease: the mechanism that drives modality choice (Stage 5). A clinical claim requiring human validation, not autonomous assertion.",
      "enum": [null, "loss_of_function_haploinsufficient", "loss_of_function_recessive", "gain_of_function", "dominant_negative", "splice", "repeat_expansion", "nonsense", "toxic_rna", "unknown"]
    },
    "causal_gene": {
      "type": ["string", "null"],
      "description": "For monogenic disease: the known causal gene (often IS the target, collapsing Stage-4 discovery to confirmation)."
    },
    "data_density": {
      "type": ["string", "null"],
      "description": "Data availability tier from data_triage(); drives the Stage-3/4 branch.",
      "enum": [null, "rich", "moderate", "sparse"]
    },
    "modality": {
      "type": ["string", "null"],
      "description": "Chosen therapeutic modality, set at Stage 5. Common-disease families + genetic-disease families.",
      "enum": [null, "antibody", "ligand_trap_binder", "small_molecule", "aso_rna", "cell_therapy", "vaccine", "enzyme", "gene_therapy", "peptide", "other", "gene_replacement", "enzyme_replacement", "aso_knockdown", "sirna_knockdown", "splice_switching_aso", "base_prime_editing", "crispr_nuclease", "readthrough"]
    },
    "lead_targets": {
      "type": "array",
      "description": "Committed lead target(s) after Stage 5 gate.",
      "items": {
        "type": "object",
        "properties": {
          "symbol": {"type": "string"},
          "rationale": {"type": "string"},
          "evidence_score": {"type": "number"}
        }
      }
    },
    "patient_priorities": {
      "type": "array",
      "description": "Ranked patient priorities from Stage 2; become design requirements.",
      "items": {"type": "object", "properties": {"priority": {"type": "string"}, "rank": {"type": "integer"}}}
    },
    "stages": {
      "type": "object",
      "description": "Per-stage status. Keys are stage ids '1'..'10'.",
      "additionalProperties": {
        "type": "object",
        "required": ["name", "status"],
        "properties": {
          "name": {"type": "string"},
          "status": {"type": "string", "enum": ["not_started", "in_progress", "complete", "skipped", "blocked"]},
          "confidence": {"type": "string", "enum": ["high", "medium", "low", "na"]},
          "skill_used": {"type": "string"},
          "artifacts": {
            "type": "array",
            "items": {"type": "object", "properties": {"filename": {"type": "string"}, "artifact_id": {"type": "string"}, "version_id": {"type": "string"}}}
          },
          "summary": {"type": "string"},
          "started_at": {"type": "string"},
          "completed_at": {"type": "string"}
        }
      }
    },
    "gates": {
      "type": "object",
      "description": "Named human-checkpoint gates. Keys are gate names from checkpoint_map.csv.",
      "additionalProperties": {
        "type": "object",
        "required": ["type", "status"],
        "properties": {
          "type": {"type": "string", "enum": ["hard", "soft"]},
          "status": {"type": "string", "enum": ["pending", "passed", "failed", "skipped"]},
          "question": {"type": "string"},
          "resolution": {"type": "string", "description": "What the user decided."},
          "resolved_at": {"type": "string"}
        }
      }
    },
    "decisions": {
      "type": "array",
      "description": "Audit log of every consequential decision + who made it.",
      "items": {
        "type": "object",
        "required": ["stage", "decision", "decided_by"],
        "properties": {
          "stage": {"type": "string"},
          "decision": {"type": "string"},
          "rationale": {"type": "string"},
          "decided_by": {"type": "string", "enum": ["user", "orchestrator"]},
          "timestamp": {"type": "string"}
        }
      }
    },
    "open_questions": {
      "type": "array",
      "description": "Unresolved uncertainties / claims needing human or clinical validation.",
      "items": {
        "type": "object",
        "properties": {
          "stage": {"type": "string"},
          "question": {"type": "string"},
          "needs": {"type": "string", "enum": ["user_input", "clinical_validation", "more_data", "expert_review"]},
          "status": {"type": "string", "enum": ["open", "resolved"]}
        }
      }
    },
    "deliverables": {
      "type": "array",
      "description": "Final outward-facing artifacts assembled at Stage 10.",
      "items": {"type": "object", "properties": {"filename": {"type": "string"}, "kind": {"type": "string"}, "artifact_id": {"type": "string"}}}
    }
  }
}