@inflexa-ai/harness 0.35.8 → 0.36.1

package/dist/contracts/target-dossier.js

@@ -1,1282 +0,0 @@
-/**
- * Target Dossier — schema-driven document produced by the
- * `executeTargetAssessment` workflow and rendered by the frontend.
- *
- * Single source of truth for the persisted JSONB shape and the rendered
- * UI shape. Both Cortex and the frontend import from this module.
- *
- * Coverage discipline: every section that depends on enrichment data
- * carries a `coverage` discriminator (`available | queried_no_data |
- * not_loaded | filtered`), taken from the shared envelope rather than
- * declared per section. `filtered` says a threshold of ours emptied the
- * section and carries the filter and the count it discarded; a partially
- * filtered `available` section carries `dropped_count`. Sections that fall
- * back to inference also carry an `inference_path`. Aggregate rows preserve
- * their contributing evidence under `evidence: [...]` arrays; rows that
- * assert a liability carry it under `support`.
- *
- * See `TARGET_DOSSIER.md` for the full editorial specification.
- */
-import { z } from "zod";
-import { OrganSystemSchema } from "./organ-system.js";
-import { SeveritySchema } from "./severity.js";
-// ── Coverage primitives ─────────────────────────────────────────────
-export const CoverageSchema = z.enum(["available", "queried_no_data", "not_loaded", "filtered"]);
-/**
- * Coverage states a per-row marker can take.
- *
- * `filtered` is a section-level outcome only: a filter that removes a row
- * removes the row, so a row that survived to be read can never report it.
- * Derived from the section vocabulary rather than restated, so the two
- * cannot drift into separate lists.
- */
-export const RowCoverageSchema = CoverageSchema.exclude(["filtered"]);
-const CoverageError = z.object({
-    message: z.string(),
-    source: z.string().optional(),
-});
-/**
- * Build a discriminated section schema: when `coverage` is `available`,
- * `data` is required and matches the inner schema. Otherwise `data` is
- * absent and an optional `error` payload may be present.
- *
- * `dropped_count` rides on the `available` branch as well as the `filtered`
- * one because a filter that removes some rows still leaves a section whose
- * list is partial — without it, a section that discarded most of its rows
- * reports a clean `available` and overstates its own completeness.
- */
-function withCoverage(data) {
-    return z.discriminatedUnion("coverage", [
-        z.object({
-            coverage: z.literal("available"),
-            data,
-            dropped_count: z.number().int().nonnegative().optional(),
-            inference_path: z.string().optional(),
-            truncated: z.boolean().optional(),
-        }),
-        z.object({
-            coverage: z.literal("queried_no_data"),
-            error: CoverageError.optional(),
-            inference_path: z.string().optional(),
-        }),
-        z.object({
-            coverage: z.literal("filtered"),
-            filter: z.string(),
-            dropped_count: z.number().int().nonnegative(),
-            inference_path: z.string().optional(),
-        }),
-        z.object({
-            coverage: z.literal("not_loaded"),
-            reason: z.string().optional(),
-        }),
-    ]);
-}
-// ── Section blurbs (renderer source of truth) ───────────────────────
-export const SECTION_BLURBS = {
-    entity: "Canonical identity for the assessed target, including ontology, identifiers, and synonyms.",
-    safety_profile: "Per-organ liabilities derived from genetic, expression, FAERS, and class-precedent evidence. Each row carries an audit trail and a mechanism hypothesis where supportable.",
-    therapeutic_area_associations: "Disease and therapeutic-area associations from genetics, literature, and Open Targets evidence rows; intended as orientation for indication selection.",
-    indications: "Candidate indications ranked by combined evidence weight; each row carries the contributing evidence sources.",
-    clinical_development: "Active and completed trials of modulators of this target, indexed from ClinicalTrials.gov.",
-    reference_biology: "Preclinical biology, expression, KO phenotype, and PPI context supporting the target's mechanistic basis.",
-    executive_recommendation: "Disposition (pursue / conditional / de-prioritize / insufficient evidence) with cited rationale, key strengths, and key risks.",
-};
-// ── Shared evidence primitives ──────────────────────────────────────
-export const EvidenceItemSchema = z.object({
-    pmid: z.string().optional(),
-    doi: z.string().optional(),
-    accession: z.string().optional(),
-    source: z.string(),
-    predicate: z.string().optional(),
-    score: z.number().optional(),
-    strength: z.string().optional(),
-    is_human: z.boolean().optional(),
-    is_clinical: z.boolean().optional(),
-    excerpt: z.string().optional(),
-    metadata: z.record(z.string(), z.unknown()).optional(),
-    regulatory_reference: z
-        .object({
-        document: z.string(),
-        section: z.string().optional(),
-        doc_id: z.string().optional(),
-        doc_url: z.string().url().optional(),
-    })
-        .optional(),
-});
-const EvidenceList = z.array(EvidenceItemSchema);
-/**
- * Evidence attached to a claim, which must resolve to something a reader can
- * actually go and check. `source` alone names a provenance bucket, not a
- * record, so it does not qualify on its own.
- *
- * The constraint lives here rather than on `EvidenceItemSchema` because that
- * shape is shared with sections whose producers legitimately carry looser
- * evidence; tightening it globally would break them, and loosening the claim
- * to match them would defeat the point.
- */
-export const ClaimEvidenceSchema = EvidenceItemSchema.refine((e) => Boolean(e.pmid ?? e.doi ?? e.accession ?? e.regulatory_reference), {
-    message: "claim evidence needs a locator: pmid, doi, accession, or regulatory_reference",
-});
-/**
- * What backs a claim: either evidence, or a stated reason there is none.
- *
- * Discriminating on `state` — rather than making `evidence` nullable and
- * checking it at runtime — is what makes a scored claim with no evidence
- * unconstructable rather than merely invalid. `unknown` is a complete,
- * first-class outcome: an invariant that is harder to satisfy honestly than
- * dishonestly makes the data worse, not better.
- */
-export const ClaimSupportSchema = z.discriminatedUnion("state", [
-    z.object({
-        state: z.literal("scored"),
-        evidence: z.array(ClaimEvidenceSchema).min(1),
-    }),
-    z.object({
-        state: z.literal("unknown"),
-        reason: z.string().min(1),
-    }),
-]);
-/**
- * Attach support to a claim body.
- *
- * The support rides as a field rather than wrapping the body, because these
- * rows *are* the assertion: a reader of an unevidenced liability still needs
- * the liability. Swapping the body out on the unknown branch would leave
- * nothing to read.
- */
-function withEvidence(body) {
-    return body.extend({ support: ClaimSupportSchema });
-}
-// ── §1.1 Entity ─────────────────────────────────────────────────────
-export const EntitySchema = z.object({
-    canonicalId: z.string(),
-    symbol: z.string(),
-    displayName: z.string(),
-    /**
-     * Cortex's Phase-0 resolver only emits `"gene"`. The schema keeps the
-     * broader enum so protein-, rna- and complex-level entities are
-     * expressible once the resolver supports them.
-     */
-    entityType: z.enum(["gene", "protein", "rna", "complex"]),
-    ontology: z.string(),
-    identifiers: z.object({
-        hgnc: z.string().optional(),
-        ensembl: z.string().optional(),
-        uniprot: z.string().optional(),
-        chembl: z.string().optional(),
-        ncbiGene: z.string().optional(),
-    }),
-    synonyms: z.array(z.string()).default([]),
-    proteinFamily: z.string().optional(),
-});
-// ── §2.1 Liability summary ──────────────────────────────────────────
-/**
- * The assertion a liability bullet makes, without its support.
- *
- * Named separately because a dropped bullet records the same assertion
- * plus the reason it was dropped, and carries no support of its own.
- */
-export const LiabilityBulletBodySchema = z.object({
-    text: z.string(),
-    rationale: z.string(),
-    category: z.enum(["fatal_post_market", "class_liability", "off_target_safety", "high_safety_organ_expression", "broad_expression", "other"]),
-});
-export const LiabilityBulletSchema = withEvidence(LiabilityBulletBodySchema);
-/**
- * Liability bullets removed post-synthesis because they cited a PMID the
- * direction-of-effect auditor found contradicts the bullet's framing.
- * Mirrors `executive_recommendation.key_risks_dropped` — the dropped
- * content is preserved with the reason for an audit trail.
- */
-export const LiabilityBulletDroppedSchema = LiabilityBulletBodySchema.extend({
-    reason: z.string(),
-    cited_pmid: z.string().optional(),
-});
-/** `.strict()` rejects the derived counters, which live in the derived sub-tree. */
-export const LiabilitySummarySchema = z
-    .object({
-    liability_bullets: z.array(LiabilityBulletSchema),
-    liability_bullets_dropped: z.array(LiabilityBulletDroppedSchema).optional(),
-    modality_recommendation: z.string().nullable(),
-    same_class_drug_count: z.number().int().nonnegative(),
-    inferred_therapeutic_area: z.string().nullable(),
-    no_liabilities_disclosure: z.string().optional(),
-})
-    .strict();
-// ── §2.2 Tractability ───────────────────────────────────────────────
-export const TractabilityModalitySchema = z.object({
-    /**
-     * Phase-4 emits `small_molecule`, `antibody`, and `other_clinical`. The
-     * remaining variants belong to the Phase-2 modality fallback (PROTAC,
-     * oligonucleotide, peptide libraries).
-     */
-    modality: z.enum(["small_molecule", "antibody", "protac", "other_clinical", "oligonucleotide", "peptide"]),
-    levels: z.array(z.string()),
-    has_approved_drug: z.boolean(),
-    has_clinical_stage: z.boolean(),
-    is_inferred_from_family: z.boolean(),
-    approved_drug_ids: z.array(z.string()).optional(),
-    note: z.string().optional(),
-});
-const MOLECULE_TYPE_TO_MODALITY = {
-    Protein: ["peptide", "antibody"],
-    "Small molecule": ["small_molecule"],
-    Oligonucleotide: ["oligonucleotide"],
-};
-export const TractabilitySchema = withCoverage(z
-    .object({
-    modalities: z.array(TractabilityModalitySchema),
-    preferred_modality: z.string().nullable(),
-    drug_molecule_types_present: z.array(z.string()).default([]),
-})
-    .superRefine((v, ctx) => {
-    for (const moleculeType of v.drug_molecule_types_present) {
-        const allowed = MOLECULE_TYPE_TO_MODALITY[moleculeType];
-        if (!allowed)
-            continue; // unknown molecule_type — skip rather than block
-        const hasMatching = v.modalities.some((m) => allowed.includes(m.modality) && !m.is_inferred_from_family);
-        if (!hasMatching) {
-            ctx.addIssue({
-                code: "custom",
-                message: `drug molecule_type "${moleculeType}" has no matching enumerated modality row`,
-                path: ["modalities"],
-            });
-        }
-    }
-}));
-// ── §2.3 Indications ────────────────────────────────────────────────
-export const IndicationRowSchema = z.object({
-    disease_id: z.string(),
-    disease_name: z.string(),
-    composite_score: z.number(),
-    composite_score_breakdown: z
-        .object({
-        base: z.number(),
-        source_bonuses: z.record(z.string(), z.number()),
-        paper_depth: z.number(),
-    })
-        .optional(),
-    evidence_score: z.number(),
-    source_count: z.number().int().nonnegative(),
-    unique_paper_count: z.number().int().nonnegative(),
-    sources: z.array(z.string()),
-    evidence: EvidenceList,
-});
-export const IndicationsSchema = withCoverage(z.object({
-    rows: z.array(IndicationRowSchema),
-    excluded_unsupported_count: z.number().int().nonnegative().optional(),
-    unsupported_associations: z
-        .array(z.object({
-        disease_id: z.string(),
-        disease_name: z.string(),
-    }))
-        .optional(),
-}));
-// ── §2.4 Drug interactions ──────────────────────────────────────────
-export const DrugInteractionRowSchema = z.object({
-    drug_id: z.string().nullable(),
-    drug_name: z.string(),
-    best_score: z.number(),
-    predicates: z.array(z.string()),
-    sources: z.array(z.string()),
-    paper_count: z.number().int().nonnegative(),
-    dominant_direction: z.enum(["positive", "negative", "mixed", "unknown"]),
-    has_human_evidence: z.boolean(),
-    has_clinical_evidence: z.boolean(),
-    evidence: EvidenceList,
-});
-export const DrugInteractionsSchema = withCoverage(z.object({ rows: z.array(DrugInteractionRowSchema) }));
-// ── §2.5 Clinical development ───────────────────────────────────────
-export const ClinicalTrialAttributionBasisSchema = z.object({
-    kind: z.enum([
-        "mechanism_target_match",
-        "known_class_drug",
-        "therapeutic_program_match",
-        "related_family_target",
-        "biomarker_endpoint",
-        "condition_only",
-        "text_match",
-        "manual",
-    ]),
-    source: z.string(),
-    excerpt: z.string().optional(),
-    metadata: z.record(z.string(), z.unknown()).optional(),
-});
-export const ResolvedTrialInterventionSchema = z.object({
-    name: z.string(),
-    intervention_type: z.string().nullable().optional(),
-    chembl_id: z.string().nullable().optional(),
-    therapeutic_program_id: z.string().nullable().optional(),
-    target_uniprots: z.array(z.string()).default([]),
-    resolver_source: z.string(),
-});
-export const ClinicalTrialAttributionSchema = z
-    .object({
-    relationship: z.enum([
-        "direct_modulator",
-        "class_modulator",
-        "related_family_target",
-        "target_biomarker",
-        "pathway_biomarker",
-        "condition_only",
-        "unrelated",
-        "unknown",
-    ]),
-    evidence_role: z.enum(["supports_target", "contextual", "excluded"]),
-    basis: z.array(ClinicalTrialAttributionBasisSchema).min(1),
-    resolved_interventions: z.array(ResolvedTrialInterventionSchema).default([]),
-    exclusion_reason: z.string().optional(),
-})
-    .superRefine((v, ctx) => {
-    if (v.evidence_role !== "supports_target" && !v.exclusion_reason) {
-        ctx.addIssue({
-            code: "custom",
-            message: "contextual/excluded trial evidence requires exclusion_reason",
-            path: ["exclusion_reason"],
-        });
-    }
-    if (v.evidence_role === "supports_target" && v.relationship !== "direct_modulator" && v.relationship !== "class_modulator") {
-        ctx.addIssue({
-            code: "custom",
-            message: "supports_target evidence must be direct_modulator or class_modulator",
-            path: ["relationship"],
-        });
-    }
-});
-export const ClinicalTrialRowSchema = z.object({
-    nct_id: z.string(),
-    title: z.string(),
-    phase: z.string().nullable(),
-    status: z.string(),
-    conditions: z.array(z.string()),
-    start_date: z.string().nullable(),
-    completion_date: z.string().nullable(),
-    match_confidence: z.enum(["high", "medium", "low", "off_target"]),
-    attribution: ClinicalTrialAttributionSchema,
-    eligible_for_toxicology_aggregation: z.boolean(),
-});
-export const TrialOutcomeRowSchema = z.object({
-    nct_id: z.string(),
-    measure: z.string(),
-    outcome_type: z.enum(["primary", "secondary", "other"]),
-    description: z.string().optional(),
-    time_frame: z.string().optional(),
-    effect: z.discriminatedUnion("kind", [
-        z.object({
-            kind: z.literal("quantitative"),
-            value: z.number(),
-            ci_low: z.number().optional(),
-            ci_high: z.number().optional(),
-            units: z.string(),
-        }),
-        z.object({
-            kind: z.literal("qualitative"),
-            direction: z.enum(["increase", "decrease", "no_change"]),
-            magnitude_label: z.string(),
-        }),
-        z.object({
-            kind: z.literal("not_extracted"),
-            reason: z.enum(["ctgov_no_numeric_result", "ctgov_no_result_groups", "parse_failure"]),
-        }),
-    ]),
-    attribution: ClinicalTrialAttributionSchema.optional(),
-    eligible_for_toxicology_aggregation: z.boolean().default(false),
-});
-const FailureCategorySchema = z.discriminatedUnion("category", [
-    z.object({ category: z.literal("safety"), safety_evidence_excerpt: z.string() }),
-    z.object({ category: z.literal("strategic"), category_evidence_excerpt: z.string() }),
-    z.object({ category: z.literal("operational"), category_evidence_excerpt: z.string() }),
-    z.object({ category: z.literal("efficacy"), category_evidence_excerpt: z.string() }),
-]);
-export const FailedTrialRowSchema = z
-    .object({
-    nct_id: z.string(),
-    title: z.string(),
-    why_stopped: z.string(),
-    classifier: z.enum(["rules", "llm"]),
-    failure_category: FailureCategorySchema,
-    attribution: ClinicalTrialAttributionSchema,
-    eligible_for_toxicology_aggregation: z.boolean(),
-})
-    .superRefine((v, ctx) => {
-    const excerpt = "safety_evidence_excerpt" in v.failure_category ? v.failure_category.safety_evidence_excerpt : v.failure_category.category_evidence_excerpt;
-    // CT.gov sometimes terminates trials without recording a `whyStopped`
-    // reason. In that case the assembler emits `why_stopped: ""` with
-    // `category: "operational"` and `excerpt: ""` — there's nothing to
-    // classify and nothing to excerpt. Both being empty is the valid
-    // "no recorded reason" shape; mismatched emptiness is an error.
-    const whyEmpty = v.why_stopped.length === 0;
-    const excerptEmpty = excerpt.length === 0;
-    if (whyEmpty !== excerptEmpty) {
-        ctx.addIssue({
-            code: "custom",
-            message: whyEmpty
-                ? `failure_category evidence_excerpt is non-empty but why_stopped is empty`
-                : `failure_category evidence_excerpt is empty but why_stopped is non-empty`,
-            path: ["failure_category"],
-        });
-        return;
-    }
-    if (whyEmpty)
-        return;
-    if (!v.why_stopped.toLowerCase().includes(excerpt.toLowerCase())) {
-        ctx.addIssue({
-            code: "custom",
-            message: `failure_category evidence_excerpt is not a substring of why_stopped`,
-            path: ["failure_category"],
-        });
-    }
-});
-export const ClinicalBenchmarksSchema = z.object({
-    therapeutic_area: z.string().nullable(),
-    fallback_to_all_areas: z.boolean(),
-    phase_transitions: z.record(z.string(), z.number()),
-    likelihood_of_approval: z.number().nullable(),
-    source_attribution: z.string(),
-});
-export const ClinicalDevelopmentSchema = z.object({
-    trials: withCoverage(z.object({
-        rows: z.array(ClinicalTrialRowSchema),
-        excluded_rows: z.array(ClinicalTrialRowSchema).default([]),
-        selection_criteria: z
-            .object({
-            derived_from: z.string().optional(),
-            min_confidence: z.string().optional(),
-            excluded_off_target_count: z.number().int().nonnegative().optional(),
-        })
-            .optional(),
-    })),
-    outcomes: withCoverage(z.object({ rows: z.array(TrialOutcomeRowSchema) })),
-    failed_trials: withCoverage(z.object({
-        rows: z.array(FailedTrialRowSchema),
-        excluded_rows: z.array(FailedTrialRowSchema).default([]),
-    })),
-    benchmarks: ClinicalBenchmarksSchema,
-});
-// ── §2.6 Safety profile ─────────────────────────────────────────────
-export const OrganRiskRowSchema = z.object({
-    organ: OrganSystemSchema,
-    risk_level: z.enum(["high", "medium", "low"]),
-    signal_type_count: z.number().int().nonnegative(),
-    signals: z.object({
-        chembl_polypharm_count: z.number().int().nonnegative(),
-        faers_count: z.number().int().nonnegative(),
-        trial_ae_count: z.number().int().nonnegative(),
-        class_liability_present: z.boolean(),
-    }),
-    evidence: EvidenceList,
-});
-const SeriousnessAvailableSchema = z
-    .object({
-    coverage: z.literal("available"),
-    total_reports: z.number().int().nonnegative(),
-    by_seriousness: z.object({
-        death: z.number().int().nonnegative(),
-        life_threatening: z.number().int().nonnegative(),
-        hospitalization: z.number().int().nonnegative(),
-        disabling: z.number().int().nonnegative(),
-        other_serious: z.number().int().nonnegative(),
-        congenital_anomaly: z.number().int().nonnegative(),
-    }),
-    fatal_report_count: z.number().int().nonnegative(),
-})
-    .superRefine((v, ctx) => {
-    // NOTE: by_seriousness categories are independent binary flags on
-    // each FAERS report — a single fatal hospitalisation increments
-    // both `death` and `hospitalization` — so sum(by_seriousness) can
-    // legitimately exceed total_reports. Do not invariant on the sum.
-    if (v.fatal_report_count > v.by_seriousness.death) {
-        ctx.addIssue({
-            code: "custom",
-            message: `fatal_report_count=${v.fatal_report_count} exceeds by_seriousness.death=${v.by_seriousness.death}`,
-            path: ["fatal_report_count"],
-        });
-    }
-    const sum = v.by_seriousness.death +
-        v.by_seriousness.life_threatening +
-        v.by_seriousness.hospitalization +
-        v.by_seriousness.disabling +
-        v.by_seriousness.other_serious +
-        v.by_seriousness.congenital_anomaly;
-    if (v.total_reports > 1000 && sum === 0) {
-        ctx.addIssue({
-            code: "custom",
-            message: `seriousness is all-zero across ${v.total_reports} reports; emit coverage:"queried_no_data" instead of fabricated zeros`,
-            path: ["by_seriousness"],
-        });
-    }
-});
-const SeriousnessQueriedNoDataSchema = z.object({
-    coverage: z.literal("queried_no_data"),
-    total_reports: z.number().int().nonnegative(),
-});
-export const FaersSummarySchema = z.object({
-    total_reports: z.number().int().nonnegative(),
-    seriousness: z.discriminatedUnion("coverage", [SeriousnessAvailableSchema, SeriousnessQueriedNoDataSchema]),
-    top_signals: z.array(z.object({
-        meddra_term: z.string(),
-        organ: z.string().optional(),
-        report_count: z.number().int().nonnegative(),
-        proportional_reporting_ratio: z.number().optional(),
-    })),
-    per_modulator: z.array(z.object({
-        modulator: z.string(),
-        modulator_id: z.string().nullable(),
-        report_count: z.number().int().nonnegative(),
-        coverage: RowCoverageSchema,
-    })),
-});
-export const TrialAesSchema = z.object({
-    serious: z.array(z.object({
-        term: z.string(),
-        incidence_pct: z.number(),
-        organ: z.string().optional(),
-        nct_ids: z.array(z.string()),
-    })),
-    non_serious: z.array(z.object({
-        term: z.string(),
-        incidence_pct: z.number(),
-        organ: z.string().optional(),
-        nct_ids: z.array(z.string()),
-    })),
-    /** Floor pct for non-serious AEs, low enough to keep real low-incidence AEs. */
-    non_serious_floor_pct: z.number().nonnegative().default(2),
-    /**
-     * Count of rows dropped by the catch-all-bucket filter (e.g., "Other"
-     * term or term equal to organ system). Surfaced for auditability.
-     */
-    dropped_uninformative_count: z.number().int().nonnegative().optional(),
-    coverage_qualifier: z
-        .object({
-        trials_queried: z.number().int().nonnegative(),
-        trials_with_ae_data: z.number().int().nonnegative(),
-        serious_floor_applied: z.number().optional(),
-        non_serious_floor_pct_applied: z.number().optional(),
-    })
-        .optional(),
-});
-const SelectivitySchema = z.union([
-    z.object({
-        vs_primary_potency: z.object({
-            primary_pchembl_used: z.number(),
-            primary_source: z.enum(["chembl_target_drug_indication", "literature_curated"]),
-            fold: z.number().positive().finite(),
-            log_units: z.number(),
-        }),
-    }),
-    z.object({
-        selectivity_unknown: z.literal(true),
-        reason: z.string().min(1),
-    }),
-]);
-/**
- * The measured facts about an off-target hit, shared by the rows that
- * assert a liability and the rows that record why one was set aside.
- */
-export const OffTargetRowBodySchema = z.object({
-    off_target_id: z.string().nullable(),
-    off_target_name: z.string(),
-    target_class: z.string().optional(),
-    pchembl: z.number(),
-    is_safety_panel_target: z.boolean(),
-    organ_system: OrganSystemSchema.nullable(),
-    clinical_consequence: z.string().nullable(),
-    selectivity: SelectivitySchema,
-    selectivity_window_below_threshold: z.boolean(),
-    metadata: z.object({ merged_chembl_ids: z.array(z.string()).optional() }).optional(),
-});
-/** The claim's own evidence rides in `support`, so the row carries no second evidence list. */
-export const OffTargetRowSchema = withEvidence(OffTargetRowBodySchema.extend({ relationship: z.literal("off_target") }));
-/**
- * Excluded rows record why something was set aside rather than asserting a
- * liability, so they carry evidence without the claim contract.
- */
-export const ExcludedOffTargetRowSchema = OffTargetRowBodySchema.extend({
-    relationship: z.enum(["intended_co_target", "on_target_self_hit", "obligate_cofactor"]),
-    reason: z.string().min(1),
-    evidence: EvidenceList,
-});
-export const OffTargetPanelSchema = z.object({
-    rows: z.array(OffTargetRowSchema),
-    excluded_rows: z.array(ExcludedOffTargetRowSchema),
-});
-export const ClassLiabilityOrganSchema = z.object({
-    organ: OrganSystemSchema,
-    drug_count_in_class: z.number().int().nonnegative(),
-    drugs_with_signal: z.number().int().nonnegative(),
-    signal_fraction: z.number(),
-    is_class_liability: z.boolean(),
-    suppressed_reason: z.string().nullable(),
-    top_aes: z.array(z.object({
-        term: z.string(),
-        report_count: z.number().int().nonnegative(),
-    })),
-});
-export const ClassPrecedentSchema = z.object({
-    drugs_in_class: z.array(z.object({
-        drug_id: z.string().nullable(),
-        drug_name: z.string(),
-        max_phase: z.number().int(),
-        mechanism: z.string().optional(),
-    })),
-    per_organ: z.array(ClassLiabilityOrganSchema),
-});
-export const SafetyFlagSchema = withEvidence(z.object({
-    organ: OrganSystemSchema,
-    trail: z.string(),
-    mechanism_hypothesis: z.string().nullable().optional(),
-    severity: SeveritySchema,
-}));
-export const RegulatoryActionRowSchema = z
-    .object({
-    drug_chembl_id: z.string(),
-    drug_name: z.string(),
-    agency: z.enum(["FDA", "EMA", "MHRA", "PMDA", "Health Canada", "TGA"]),
-    action_kind: z.enum(["referral", "withdrawal", "indication_restriction", "REMS", "black_box", "DHCP", "safety_communication", "label_warning"]),
-    action_date: z.string(),
-    finding: z.string(),
-    source_url: z.string().url().optional(),
-    source_kind: z.enum(["label_warning", "referral", "rems", "withdrawal", "boxed_warning", "safety_communication"]),
-    application_number: z.string().optional(),
-    label_section: z.string().optional(),
-    source_date: z.string().optional(),
-    evidence: EvidenceList,
-})
-    .superRefine((v, ctx) => {
-    if (v.source_kind === "label_warning" && v.action_kind === "safety_communication") {
-        ctx.addIssue({
-            code: "custom",
-            message: "FDA label warnings must not be represented as action_kind:safety_communication",
-            path: ["action_kind"],
-        });
-    }
-});
-/**
- * One warning fragment from an FDA label, attributed to a canonical organ.
- *
- * The application number plus the label section are what let a reader open the
- * label and find the excerpt again, which is why the row carries both rather
- * than a bare drug name.
- */
-export const RegulatoryOrganSignalRowSchema = withEvidence(z.object({
-    organ: OrganSystemSchema,
-    drug_name: z.string(),
-    agency: z.literal("FDA"),
-    application_number: z.string(),
-    label_section: z.string(),
-    excerpt: z.string(),
-}));
-export const RegulatoryOrganSignalsSchema = withCoverage(z.object({ rows: z.array(RegulatoryOrganSignalRowSchema) }));
-export const SafetyProfileSchema = z.object({
-    organ_rollup: withCoverage(z.object({ rows: z.array(OrganRiskRowSchema) })),
-    faers: withCoverage(FaersSummarySchema),
-    trial_aes: withCoverage(TrialAesSchema),
-    off_target_panel: withCoverage(OffTargetPanelSchema),
-    failed_trials_safety_lens: withCoverage(z.object({
-        rows: z.array(FailedTrialRowSchema),
-        excluded_rows: z.array(FailedTrialRowSchema).default([]),
-    })),
-    class_precedent: withCoverage(ClassPrecedentSchema),
-    target_organ_liabilities: withCoverage(z.object({ rows: z.array(SafetyFlagSchema) })),
-    regulatory_actions: withCoverage(z.object({ rows: z.array(RegulatoryActionRowSchema) })).optional(),
-    regulatory_organ_signals: RegulatoryOrganSignalsSchema.optional(),
-});
-// ── §2.6a Safety corroboration spine ────────────────────────────────
-/**
- * One source's signal for one organ.
- *
- * The source names itself in a field rather than occupying a field of its own.
- * That is what keeps the contributing set open: a source that did not exist
- * when this shape was written contributes by emitting a record, with no schema
- * edit, no new branch, and no consumer change. A struct with one field per
- * source would instead force a schema change per source — and, because a new
- * source arriving before its field exists has nowhere to land, would invite a
- * second, narrower evidence path alongside this one.
- *
- * `evidence` is claim evidence, so a contribution always resolves to a record a
- * reader can go and check.
- */
-export const OrganSignalContributionSchema = z.object({
-    /** Stable id of the source that produced the signal. */
-    source: z.string().min(1),
-    /** What this source says about the organ, in the source's own terms. */
-    signal: z.string().min(1),
-    evidence: ClaimEvidenceSchema,
-});
-/**
- * The corroboration record for one organ: which sources carry a signal for it,
- * how many of them are independent, and what each contributed.
- *
- * `independent_source_count` counts distinct source ids, not contributions — a
- * source carrying three label warnings for one organ is still one source. The
- * claim's evidence is the contributions' evidence, which is why a signal with
- * no locator is never admitted as a contribution in the first place.
- */
-export const OrganCorroborationRowSchema = withEvidence(z.object({
-    organ: OrganSystemSchema,
-    contributions: z.array(OrganSignalContributionSchema).min(1),
-    corroborating_sources: z.array(z.string().min(1)).min(1),
-    independent_source_count: z.number().int().positive(),
-}));
-/**
- * `dropped_count` on this section counts *signals* — the fold's input unit —
- * discarded because their organ did not resolve, because they carried no
- * locator, or because their organ drew fewer than `min_independent_sources`
- * distinct sources.
- */
-export const SafetyCorroborationSchema = withCoverage(z.object({
-    rows: z.array(OrganCorroborationRowSchema),
-    /** Every source id that offered at least one signal on this run. */
-    sources_considered: z.array(z.string().min(1)),
-    /** Distinct sources an organ needed to be reported as corroborated. */
-    min_independent_sources: z.number().int().positive(),
-}));
-// ── §2.6b Claim investigation ───────────────────────────────────────
-/**
- * What became of a claim once it was argued against.
- *
- * Four words, no number. A numeric soundness would need a threshold to mean
- * anything, and a threshold on this axis deletes real liabilities: the organs
- * with the thinnest published mechanism are routinely the ones worth the most
- * attention. `undetermined` is a real outcome — the argument ran and settled
- * nothing — not a failure to produce one of the other three.
- */
-export const ClaimVerdictSchema = z.enum(["upheld", "weakened", "overturned", "undetermined"]);
-/** Which stopping condition ended a claim's investigation. */
-export const InvestigationConvergenceSchema = z.enum(["verdict_terminal", "verdict_settled", "round_bound_reached"]);
-/** How the target is proposed to produce the liability in an organ. */
-export const MechanismProposalSchema = withEvidence(z.object({ statement: z.string().min(1) }));
-/**
- * The case against the claim.
- *
- * Its `support` is the counter-evidence, held to the same contract as the claim
- * it attacks: an objection that cannot cite a record is `unknown` with a reason,
- * which is what stops "no supporting literature was found" being dressed up as a
- * finding of its own.
- */
-export const ClaimCritiqueSchema = withEvidence(z.object({ objection: z.string().min(1) }));
-/**
- * One organ claim, after interrogation.
- *
- * The row's own `support` backs the **verdict** — the assertion the row exists
- * to make. The mechanism and the critique are nested claims carrying their own
- * support, because they are separate assertions that can independently fail to
- * be evidenced; flattening all three onto one `support` would make it
- * unreadable which of them it was for.
- *
- * `critique` is singular: objections are deduplicated by organ, so a later
- * round's critique replaces the earlier one it was written against, and
- * `rounds_run` says how many passes it took.
- */
-export const InvestigatedClaimRowSchema = withEvidence(z.object({
-    organ: OrganSystemSchema,
-    /** Null when no mechanism was proposable from the evidence collected. */
-    mechanism: MechanismProposalSchema.nullable(),
-    /** Null when the critique step produced no objection worth recording. */
-    critique: ClaimCritiqueSchema.nullable(),
-    verdict: ClaimVerdictSchema,
-    rounds_run: z.number().int().positive(),
-    convergence: InvestigationConvergenceSchema,
-}));
-/** Why a candidate organ claim produced no investigated row. */
-export const UninvestigatedClaimReasonSchema = z.enum(["not_corroborated", "exceeded_claim_budget", "investigation_unavailable"]);
-export const UninvestigatedClaimSchema = z.object({
-    organ: OrganSystemSchema,
-    reason: UninvestigatedClaimReasonSchema,
-    detail: z.string().min(1),
-});
-/**
- * The investigation record.
- *
- * `not_investigated` is part of the data rather than a diagnostic beside it: a
- * run that investigated nothing still has something to say, and it is the only
- * thing that case has to say. That is why `rows` may be empty on an `available`
- * section — every candidate that produced no row is named here with its reason.
- *
- * The two bounds ride in the section because they are what a reader needs to
- * know how hard each claim was pushed, and they are configuration, so the value
- * in force is not derivable from the code a reader happens to be looking at.
- */
-export const ClaimInvestigationSchema = withCoverage(z.object({
-    rows: z.array(InvestigatedClaimRowSchema),
-    not_investigated: z.array(UninvestigatedClaimSchema),
-    /** Propose → critique → re-verify rounds a single claim was allowed. */
-    round_bound: z.number().int().positive(),
-    /** Corroborated claims this run was allowed to investigate. */
-    claim_budget: z.number().int().positive(),
-}));
-// ── §2.7 Off-tissue risk ────────────────────────────────────────────
-export const OffTissueRowSchema = withEvidence(z.object({
-    tissue: z.string(),
-    organ: OrganSystemSchema,
-    tpm: z.number(),
-}));
-export const OffTissueRiskSchema = withCoverage(z.object({ rows: z.array(OffTissueRowSchema) }));
-// ── §3.1–3.6 Reference biology — keyed evidence sections ────────────
-export const KeyedEvidenceRowSchema = z.object({
-    partner_id: z.string().nullable(),
-    partner_name: z.string(),
-    predicate: z.string(),
-    best_score: z.number(),
-    source_count: z.number().int().nonnegative(),
-    paper_count: z.number().int().nonnegative(),
-    evidence: EvidenceList,
-});
-export const DiseaseAssociationsSchema = withCoverage(z.object({ rows: z.array(KeyedEvidenceRowSchema) }));
-export const MolecularInteractionsSchema = withCoverage(z.object({ rows: z.array(KeyedEvidenceRowSchema) }));
-export const BiomarkerEvidenceRowSchema = KeyedEvidenceRowSchema.extend({
-    metrics: z.object({
-        sensitivity: z.number().optional(),
-        specificity: z.number().optional(),
-        auc: z.number().optional(),
-        hazard_ratio: z.number().optional(),
-    }),
-});
-export const BiomarkerPotentialSchema = withCoverage(z.object({ rows: z.array(BiomarkerEvidenceRowSchema) }));
-export const ResistanceEvidenceSchema = withCoverage(z.object({ rows: z.array(KeyedEvidenceRowSchema) }));
-export const CombinationEvidenceSchema = withCoverage(z.object({ rows: z.array(KeyedEvidenceRowSchema) }));
-// ── §3.4 Genetic alterations ────────────────────────────────────────
-export const SomaticMutationRowSchema = z.object({
-    cancer_type: z.string(),
-    cohort: z.string(),
-    mutation_count: z.number().int().nonnegative(),
-    total_samples: z.number().int().nonnegative(),
-    frequency: z.number(),
-    source: z.string(),
-});
-export const ClinvarVariantRowSchema = z.object({
-    variant_id: z.string(),
-    hgvs: z.string(),
-    classification: z.string(),
-    condition: z.string(),
-    review_status: z.string(),
-});
-export const GeneticAlterationsSchema = z.object({
-    somatic: withCoverage(z.object({ rows: z.array(SomaticMutationRowSchema) })),
-    clinvar: withCoverage(z.object({ rows: z.array(ClinvarVariantRowSchema) })),
-});
-// ── §3.7 Pathway context ────────────────────────────────────────────
-export const PathwayRowSchema = z.object({
-    pathway_id: z.string(),
-    pathway_name: z.string(),
-    database: z.enum(["reactome", "kegg", "wikipathways", "msigdb"]),
-    evidence_score: z.number(),
-    entity_uniprots: z.array(z.string()).optional(),
-    metadata: z.record(z.string(), z.unknown()).optional(),
-});
-export const PathwayContextSchema = withCoverage(z.object({
-    rows: z.array(PathwayRowSchema),
-    databases_queried: z.array(z.string()),
-    databases_skipped: z.array(z.string()),
-}));
-// ── §3.8 PPI network ────────────────────────────────────────────────
-export const PpiPartnerRowSchema = z.object({
-    partner_id: z.string().nullable(),
-    partner_name: z.string(),
-    string_score: z.number().nullable(),
-    literature_score: z.number().nullable(),
-    combined_score: z.number(),
-    sources: z.array(z.string()),
-    has_human_evidence: z.boolean(),
-    has_clinical_evidence: z.boolean(),
-});
-export const PpiNetworkSchema = withCoverage(z.object({ partners: z.array(PpiPartnerRowSchema) }));
-// ── §3.9 Normal tissue expression ───────────────────────────────────
-/** Source and unit travel together, and the normalization note is mandatory. */
-export const NormalTissueExpressionSchema = z
-    .object({
-    source: z.enum(["gtex", "hpa_consensus", "hpa_rna_tissue"]),
-    unit: z.enum(["tpm", "ntpm", "consensus_normalized"]),
-    normalization_notes: z.string().min(1),
-    rows: z.array(z.object({
-        tissue: z.string(),
-        value: z.number(),
-        percentile_rank: z.number().optional(),
-    })),
-})
-    .superRefine((v, ctx) => {
-    if (v.unit === "tpm" && v.source !== "gtex") {
-        ctx.addIssue({
-            code: "custom",
-            message: `unit:"tpm" is only valid with source:"gtex" (got source:"${v.source}")`,
-            path: ["unit"],
-        });
-    }
-    if (v.unit === "ntpm" && !(v.source === "hpa_rna_tissue" || v.source === "hpa_consensus")) {
-        ctx.addIssue({
-            code: "custom",
-            message: `unit:"ntpm" is only valid with HPA sources`,
-            path: ["unit"],
-        });
-    }
-});
-// ── §3.10 Preclinical ───────────────────────────────────────────────
-export const KoPhenotypeSchema = z.object({
-    marker_symbol: z.string().nullable(),
-    viability: z.string().nullable(),
-    sex_dimorphism: z.boolean(),
-    organ_systems_with_phenotype: z.array(OrganSystemSchema),
-    top_mp_terms: z.array(z.string()),
-    total_phenotype_count: z.number().int().nonnegative(),
-    pre_weaning_lethal: z.boolean(),
-    supporting_literature: EvidenceList,
-});
-const ExpressionRank = z.enum(["absent", "low", "medium", "high", "no_data", "not_loaded"]);
-export const ExpressionHeatmapCellSchema = z.object({
-    tissue: z.string(),
-    species: z.enum(["human", "mouse", "rat", "macaque", "dog"]),
-    rank: ExpressionRank,
-});
-export const ExpressionHeatmapSchema = z.object({
-    cells: z.array(ExpressionHeatmapCellSchema),
-    per_species_coverage: z.record(z.string(), CoverageSchema),
-});
-export const TranslationalCommentaryRowSchema = z.object({
-    severity: z.enum(["ok", "caution", "gap"]),
-    organ: z.string().optional(),
-    species: z.string().optional(),
-    text: z.string(),
-});
-export const PreclinicalLiteratureRowSchema = z.object({
-    pmid: z.string().nullable(),
-    claim: z.string(),
-    excerpt: z.string().optional(),
-    model_system: z.string(),
-    species: z.string(),
-});
-export const PreclinicalDataCoverageSchema = z.object({
-    ko: z.enum(["available", "no_phenotypes", "none", "queried_no_data", "not_loaded"]),
-    expression: CoverageSchema,
-    literature: CoverageSchema,
-    per_species: z.record(z.string(), z.boolean()),
-});
-export const PreclinicalProfileSchema = z.object({
-    ko_phenotype: withCoverage(KoPhenotypeSchema),
-    expression_heatmap: withCoverage(ExpressionHeatmapSchema),
-    translational_commentary: withCoverage(z.object({ rows: z.array(TranslationalCommentaryRowSchema) })),
-    preclinical_literature: withCoverage(z.object({
-        rows: z.array(PreclinicalLiteratureRowSchema),
-        total_claim_count: z.number().int().nonnegative(),
-        truncated: z.boolean(),
-    })),
-    data_coverage: PreclinicalDataCoverageSchema,
-});
-// ── §3.11 Key papers ────────────────────────────────────────────────
-export const KeyPaperRowSchema = z.object({
-    pmid: z.string(),
-    title: z.string(),
-    internal_reference_count: z.number().int().nonnegative(),
-    year: z.number().int().optional(),
-});
-export const KeyPapersSchema = withCoverage(z.object({ rows: z.array(KeyPaperRowSchema) }));
-// ── §4.1 Evidence conflicts ─────────────────────────────────────────
-export const EvidenceConflictRowSchema = z.object({
-    evidence_item_id: z.string(),
-    predicate: z.string(),
-    contradicting_predicates: z.array(z.string()),
-    surfaced_in_section: z.string(),
-    evidence: EvidenceList,
-});
-export const EvidenceConflictsSchema = withCoverage(z.object({ rows: z.array(EvidenceConflictRowSchema) }));
-// ── §4.2 Evidence timeline ──────────────────────────────────────────
-export const EvidenceTimelineSchema = withCoverage(z.object({
-    histogram: z.record(z.string(), z.number().int().nonnegative()),
-    first_reported_year: z.number().int().nullable(),
-    last_reported_year: z.number().int().nullable(),
-    trend_labels: z.array(z.string()),
-}));
-// ── §4.3 Translational chain ────────────────────────────────────────
-const TranslationalTier = z.enum(["computational", "basic_in_vitro", "complex_in_vitro", "in_vivo_animal", "ex_vivo_human", "clinical"]);
-export const TranslationalChainSchema = withCoverage(z.object({
-    tiers: z.array(z.object({
-        tier: TranslationalTier,
-        claim_count: z.number().int().nonnegative(),
-        paper_count: z.number().int().nonnegative(),
-    })),
-    peak_evidence_tier: TranslationalTier.nullable(),
-    progression_complete: z.boolean(),
-    weakest_progression_gap: TranslationalTier.nullable().optional(),
-}));
-// ── §4.4 Additional evidence ────────────────────────────────────────
-export const AdditionalEvidenceSchema = withCoverage(z.object({
-    rows: z.array(z.object({
-        predicate: z.string(),
-        evidence: EvidenceList,
-    })),
-    score_floor: z.number(),
-}));
-// ── §4.5 Discovery trials ───────────────────────────────────────────
-export const DiscoveryTrialRowSchema = z
-    .object({
-    nct_id: z.string(),
-    title: z.string(),
-    phase: z.string().nullable().optional(),
-    status: z.string().optional(),
-    conditions: z.array(z.string()),
-    start_date: z.string().optional(),
-    completion_date: z.string().optional(),
-    match_confidence: z.enum(["high", "medium", "low"]),
-    relevance_basis: z.discriminatedUnion("kind", [
-        z.object({
-            kind: z.literal("drug_in_class_match"),
-            drug_id: z.string(),
-            matched_term: z.string().optional(),
-        }),
-        z.object({ kind: z.literal("title_keyword"), matched_term: z.string() }),
-        z.object({ kind: z.literal("condition_match"), matched_term: z.string().optional() }),
-        z.object({ kind: z.literal("manual") }),
-    ]),
-    attribution: ClinicalTrialAttributionSchema,
-    eligible_for_toxicology_aggregation: z.boolean(),
-})
-    .superRefine((v, ctx) => {
-    // Low-confidence rows that only match by condition (no drug link) are unreliable;
-    // collector must drop them rather than emitting them.
-    if (v.match_confidence === "low" && v.relevance_basis.kind === "condition_match") {
-        ctx.addIssue({
-            code: "custom",
-            message: `low-confidence rows must not have relevance_basis.kind="condition_match" without an intervention drug match (drop at collector)`,
-            path: ["relevance_basis"],
-        });
-    }
-});
-export const DiscoveryTrialsSchema = withCoverage(z.object({
-    rows: z.array(DiscoveryTrialRowSchema),
-    excluded_rows: z.array(DiscoveryTrialRowSchema).default([]),
-}));
-// ── §1.0 Executive recommendation ───────────────────────────────────
-export const ExecutiveRecommendationDataSchema = z.object({
-    disposition: z.enum(["pursue", "conditional", "de_prioritize", "insufficient_evidence"]),
-    confidence: z.enum(["high", "medium", "low"]),
-    rationale: z.string(),
-    key_strengths: z.array(z.string()).max(8).default([]),
-    key_risks: z.array(z.string()).max(8).default([]),
-    key_risks_dropped: z
-        .array(z.object({
-        text: z.string(),
-        reason: z.string(),
-        cited_pmid: z.string().optional(),
-    }))
-        .optional(),
-    modality_choice: z.object({
-        modality: z.string(),
-        rationale: z.string(),
-    }),
-    coverage_qualifier: z.object({
-        sections_consulted: z.array(z.string()).default([]),
-        sections_unavailable: z.array(z.string()).default([]),
-        note: z.string(),
-        unverified_bullets: z
-            .array(z.object({
-            text: z.string(),
-            bullet_category: z.string(),
-            surface: z.literal("organ_claim_without_probe_pass"),
-        }))
-            .optional(),
-    }),
-});
-export const ExecutiveRecommendationSchema = withCoverage(ExecutiveRecommendationDataSchema);
-// ── §4.6 Synthesis diagnostics ──────────────────────────────────────
-export const SynthesisDiagnosticRowSchema = z.object({
-    step_id: z.enum(["liability-bullets", "safety-flags-trail", "translational-commentary", "dossier-recommendation"]),
-    model_id: z.string(),
-    attempt_count: z.number().int().min(1).max(2),
-    retry_critique: z.string().nullable(),
-    output_chars: z.number().int().nonnegative(),
-    probe_verdict: z.enum([
-        "pass",
-        "fail-length",
-        "fail-section-references",
-        "fail-key-strengths-risks",
-        "fail-source-references",
-        "fail-numeric-claim",
-        "fail-voice",
-        "relaxed",
-        "skipped",
-    ]),
-    final_coverage: CoverageSchema.extract(["available", "queried_no_data"]),
-    error_kind: z.enum(["synthesis-too-shallow", "synthesis-unavailable", "voice-violation"]).nullable().optional(),
-    error_message: z.string().nullable().optional(),
-});
-export const SynthesisDiagnosticsSchema = withCoverage(z.object({ rows: z.array(SynthesisDiagnosticRowSchema) }));
-// ── §4.7 Recommendation citation audit ──────────────────────────────
-export const RecommendationAuditEntrySchema = z.union([
-    z.object({
-        surface: z.enum(["rationale", "key_strengths", "key_risks", "modality_choice"]),
-        path: z.string(),
-        excerpt: z.string(),
-    }),
-    z.object({
-        surface: z.literal("external_missing"),
-        id: z.string(),
-        excerpt: z.string(),
-    }),
-    z.object({
-        surface: z.literal("organ_claim_without_probe_pass"),
-        excerpt: z.string(),
-        bullet_category: z.string(),
-    }),
-    z.object({
-        surface: z.literal("nct_wrong_class"),
-        id: z.string(),
-        excerpt: z.string(),
-    }),
-    z.object({
-        surface: z.literal("pmid_not_in_key_papers"),
-        id: z.string(),
-        excerpt: z.string(),
-    }),
-    z.object({
-        surface: z.literal("direction_mismatch"),
-        pmid: z.string(),
-        excerpt: z.string(),
-        paper_conclusion_direction: z.enum(["supports", "contradicts", "ambiguous"]).optional(),
-    }),
-    z.object({
-        surface: z.literal("abstract_unavailable"),
-        pmid: z.string(),
-        excerpt: z.string(),
-    }),
-    z.object({
-        surface: z.literal("off_topic_citation"),
-        pmid: z.string(),
-        excerpt: z.string(),
-    }),
-]);
-export const RecommendationAuditSchema = withCoverage(z.object({
-    citations_total: z.number().int().nonnegative(),
-    citations_unresolved: z.array(RecommendationAuditEntrySchema),
-    non_dossier_citations: z.array(z.object({ token: z.string(), source: z.string() })),
-}));
-// ── §4.8 Quality gates ──────────────────────────────────────────────
-export const QualityGateStatusSchema = z.object({
-    gate_id: z.string(),
-    status: z.enum(["pass", "warning", "blocked"]),
-    message: z.string(),
-    affected_sections: z.array(z.string()).default([]),
-    unresolved_count: z.number().int().nonnegative().optional(),
-    metadata: z.record(z.string(), z.unknown()).optional(),
-});
-export const QualityGatesSchema = withCoverage(z.object({ rows: z.array(QualityGateStatusSchema) }));
-// ── Composite shapes ────────────────────────────────────────────────
-export const ReferenceBiologyShape = z.object({
-    therapeutic_area_associations: DiseaseAssociationsSchema,
-    molecular_interactions: MolecularInteractionsSchema,
-    biomarker_potential: BiomarkerPotentialSchema,
-    genetic_alterations: GeneticAlterationsSchema,
-    resistance_evidence: ResistanceEvidenceSchema,
-    combination_evidence: CombinationEvidenceSchema,
-    pathway_context: PathwayContextSchema,
-    ppi_network: PpiNetworkSchema,
-    normal_tissue_expression: withCoverage(NormalTissueExpressionSchema),
-    preclinical: PreclinicalProfileSchema,
-    key_papers: KeyPapersSchema,
-});
-const AnalyticsShape = z.object({
-    evidence_conflicts: EvidenceConflictsSchema,
-    evidence_timeline: EvidenceTimelineSchema,
-    translational_chain: TranslationalChainSchema,
-    additional_evidence: AdditionalEvidenceSchema,
-    discovery_trials: DiscoveryTrialsSchema,
-    synthesis_diagnostics: SynthesisDiagnosticsSchema,
-    quality_gates: QualityGatesSchema,
-    recommendation_audit: RecommendationAuditSchema.optional(),
-});
-// ── Derived sub-tree ────────────────────────────────────────────────
-//
-// Shape produced by computeDerivedFields(body) and validated at phase-5
-// persist. `.strict()` rejects unknown keys to prevent accidental extras.
-export const DerivedSchema = z
-    .object({
-    summary: z.object({
-        has_human_evidence: z.boolean(),
-        has_clinical_evidence: z.boolean(),
-        total_evidence_items: z.number().int().nonnegative(),
-        total_distinct_papers: z.number().int().nonnegative(),
-        total_distinct_clinical_trials: z.number().int().nonnegative(),
-        strongest_strength_label: z.string().nullable(),
-        highest_score: z.number().nullable(),
-        highest_score_is_conflicted: z.boolean(),
-    }),
-    risk_summary: z.object({
-        any_fatal_signal: z.union([z.boolean(), z.literal("unknown")]),
-        highest_risk_organ: OrganSystemSchema.nullable(),
-        off_target_safety_target_hits: z.number().int().nonnegative(),
-        class_liability_count: z.number().int().nonnegative(),
-    }),
-    liability_summary: z.object({
-        counts: z.object({
-            class_liability_count: z.number().int().nonnegative(),
-            safety_target_off_target_count: z.number().int().nonnegative(),
-            off_tissue_risk_organ_count: z.number().int().nonnegative(),
-        }),
-        expression_breadth: z.object({
-            total_assessed_tissues: z.number().int().nonnegative(),
-            high_expression_tissue_count: z.number().int().nonnegative(),
-        }),
-        same_class_drug_count: z.number().int().nonnegative(),
-        safety_data_sources_checked: z.number().int().nonnegative(),
-    }),
-    organ_rollup_completeness: z
-        .object({
-        expected_organs: z.array(OrganSystemSchema),
-        present_organs: z.array(OrganSystemSchema),
-        missing_organs: z.array(OrganSystemSchema),
-    })
-        .refine((v) => v.missing_organs.length === 0, {
-        message: "missing_organs must be empty for the dossier to ship",
-        path: ["missing_organs"],
-    }),
-})
-    .strict();
-// ── Top-level Dossier ───────────────────────────────────────────────
-export const DossierSchema = z.object({
-    entity: EntitySchema,
-    generated_at: z.string(),
-    liability_summary: LiabilitySummarySchema,
-    tractability: TractabilitySchema,
-    indications: IndicationsSchema,
-    drug_interactions: DrugInteractionsSchema,
-    clinical_development: ClinicalDevelopmentSchema,
-    safety_profile: SafetyProfileSchema,
-    safety_corroboration: SafetyCorroborationSchema,
-    claim_investigation: ClaimInvestigationSchema,
-    off_tissue_risk: OffTissueRiskSchema,
-    off_target_panel: withCoverage(OffTargetPanelSchema),
-    reference_biology: ReferenceBiologyShape,
-    analytics: AnalyticsShape,
-    executive_recommendation: ExecutiveRecommendationSchema,
-    derived: DerivedSchema,
-});
-/**
- * Everything the Phase-4 assembler is responsible for building, without the
- * derived sub-tree. Phase-5 persist computes derived from the stamped body
- * and validates the complete dossier against `DossierSchema`.
- */
-export const DossierBodySchema = DossierSchema.omit({ derived: true });
-// ── Type guards ─────────────────────────────────────────────────────
-export function isDossier(value) {
-    return DossierSchema.safeParse(value).success;
-}
-/** JSON Schema export for runtime validation in non-TS environments. */
-export function dossierJsonSchema() {
-    return z.toJSONSchema(DossierSchema);
-}
-// ── Progress events ─────────────────────────────────────────────────
-export const TargetAssessmentPhaseSchema = z.enum([
-    "resolving",
-    "collecting",
-    "deciding",
-    "fanning_out",
-    "assembling",
-    "synthesizing",
-    "completed",
-    "failed",
-    "suspended",
-]);
-export const TargetAssessmentProgressEventSchema = z.object({
-    phase: TargetAssessmentPhaseSchema,
-    message: z.string(),
-    percent: z.number().min(0).max(100),
-    at: z.string(),
-});