agent-bober 0.17.1 → 0.18.0

package/dist/medical/numerics.d.ts

@@ -0,0 +1,66 @@
+/**
+ * NumericsQueryLayer — deterministic closed-whitelist numeric primitives (Phase 6, Sprint 4).
+ *
+ * ADR-3: The LLM NEVER performs arithmetic. All numeric computations are pure TypeScript
+ * over a CLOSED whitelist: mean | min | max | latest | delta | slope | percentile | zscore.
+ * Adding a computation requires extending NumericPrimitive (a code review event), not a
+ * model decision. `sampleCount: 0` signals upstream abstention.
+ *
+ * NO async. NO fs. NO network. NO LLM import. NO dynamic execution. NO subprocess.
+ * Identical input => identical output.
+ *
+ * Primitive formulas documented below (also satisfies contract assumptions line 75):
+ *
+ * mean        — sum(values) / n
+ * min         — Math.min(...values)
+ * max         — Math.max(...values)
+ * latest      — value at the maximum t_start (last element of ASC-ordered array)
+ * delta       — latest − earliest = values[n-1] − values[0]
+ * slope       — least-squares slope over (t, value) where t = Date.parse(r.tStart) epoch-ms.
+ *               formula: (n·Σ(t·v) − Σt·Σv) / (n·Σ(t²) − (Σt)²)
+ *               degenerate: denominator === 0 (all same timestamp) → value: null, sampleCount: n
+ * percentile  — linear interpolation between closest ranks (sorted ascending):
+ *               rank = (p/100) · (n−1); lo = floor(rank); hi = ceil(rank);
+ *               result = v[lo] + (rank − lo) · (v[hi] − v[lo])
+ *               (for p50, [10,20,30,40] → rank=1.5 → 20 + 0.5·10 = 25)
+ * zscore      — (latest − mean) / populationStddev
+ *               populationStddev = sqrt(Σ(v − mean)² / n)
+ *               sampleCount < 2 → abstain (stddev undefined for n=1, zero for n=0)
+ *               ([10,20,30,40]: mean=25, popStd=√125≈11.1803, z=(40-25)/11.1803≈1.3416)
+ */
+import type { HealthDataStore } from "./health-store.js";
+import type { NumericPrimitive, NumericResult, MetricWindow, LabTrend } from "./types.js";
+/**
+ * Provides deterministic, LLM-free numeric aggregations over HealthDataStore.
+ *
+ * All methods are SYNCHRONOUS. No async, no fs, no network, no LLM import.
+ * The LLM never performs arithmetic — this layer does.
+ */
+export declare class NumericsQueryLayer {
+    private readonly store;
+    constructor(store: HealthDataStore);
+    /**
+     * Compute a numeric primitive over the observations in the given time window.
+     *
+     * Abstain conditions (return { value: null, sampleCount: 0 } without throwing):
+     *   - Empty window (no rows in the time range) — sc-4-6
+     *   - Heterogeneous units across rows — sc-4-7 (cross-unit refusal)
+     *
+     * Partial abstain (value: null, sampleCount: n):
+     *   - zscore with sampleCount < 2 (stddev undefined)
+     *   - slope with degenerate denominator (all same timestamp)
+     *
+     * @param window   — metric + ISO-8601 time range
+     * @param primitive — one of the 8 whitelisted NumericPrimitive values
+     * @param percentile — percentile p ∈ [0,100], used only for "percentile" primitive (default 50)
+     */
+    getMetric(window: MetricWindow, primitive: NumericPrimitive, percentile?: number): NumericResult;
+    /**
+     * Build a LabTrend summary for a biomarker series.
+     *
+     * Abstains (latestValue: null, slope: null) when sampleCount === 0 (sc-4-6).
+     * slope is null when sampleCount < 2 (not enough data for least-squares).
+     */
+    getLabTrend(biomarker: string): LabTrend;
+}
+//# sourceMappingURL=numerics.d.ts.map

package/dist/medical/numerics.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/numerics.js

@@ -0,0 +1,216 @@
+/**
+ * NumericsQueryLayer — deterministic closed-whitelist numeric primitives (Phase 6, Sprint 4).
+ *
+ * ADR-3: The LLM NEVER performs arithmetic. All numeric computations are pure TypeScript
+ * over a CLOSED whitelist: mean | min | max | latest | delta | slope | percentile | zscore.
+ * Adding a computation requires extending NumericPrimitive (a code review event), not a
+ * model decision. `sampleCount: 0` signals upstream abstention.
+ *
+ * NO async. NO fs. NO network. NO LLM import. NO dynamic execution. NO subprocess.
+ * Identical input => identical output.
+ *
+ * Primitive formulas documented below (also satisfies contract assumptions line 75):
+ *
+ * mean        — sum(values) / n
+ * min         — Math.min(...values)
+ * max         — Math.max(...values)
+ * latest      — value at the maximum t_start (last element of ASC-ordered array)
+ * delta       — latest − earliest = values[n-1] − values[0]
+ * slope       — least-squares slope over (t, value) where t = Date.parse(r.tStart) epoch-ms.
+ *               formula: (n·Σ(t·v) − Σt·Σv) / (n·Σ(t²) − (Σt)²)
+ *               degenerate: denominator === 0 (all same timestamp) → value: null, sampleCount: n
+ * percentile  — linear interpolation between closest ranks (sorted ascending):
+ *               rank = (p/100) · (n−1); lo = floor(rank); hi = ceil(rank);
+ *               result = v[lo] + (rank − lo) · (v[hi] − v[lo])
+ *               (for p50, [10,20,30,40] → rank=1.5 → 20 + 0.5·10 = 25)
+ * zscore      — (latest − mean) / populationStddev
+ *               populationStddev = sqrt(Σ(v − mean)² / n)
+ *               sampleCount < 2 → abstain (stddev undefined for n=1, zero for n=0)
+ *               ([10,20,30,40]: mean=25, popStd=√125≈11.1803, z=(40-25)/11.1803≈1.3416)
+ */
+// ── Internal computation helpers ──────────────────────────────────────
+/**
+ * Compute the least-squares slope over (epoch-ms timestamp, value) pairs.
+ * Returns null when the denominator is zero (all observations at the same timestamp).
+ */
+function leastSquaresSlope(rows) {
+    const n = rows.length;
+    const ts = rows.map((r) => Date.parse(r.tStart));
+    const vs = rows.map((r) => r.value);
+    let sumT = 0;
+    let sumV = 0;
+    let sumTV = 0;
+    let sumT2 = 0;
+    for (let i = 0; i < n; i++) {
+        sumT += ts[i];
+        sumV += vs[i];
+        sumTV += ts[i] * vs[i];
+        sumT2 += ts[i] * ts[i];
+    }
+    const denom = n * sumT2 - sumT * sumT;
+    if (denom === 0)
+        return null; // all same timestamp — slope undefined
+    return (n * sumTV - sumT * sumV) / denom;
+}
+/**
+ * Linear interpolation percentile on the sorted-ascending values.
+ * rank = (p/100) · (n−1); result = v[lo] + (rank − lo) · (v[hi] − v[lo]).
+ * p must be in [0, 100].
+ */
+function linearPercentile(sortedValues, p) {
+    const n = sortedValues.length;
+    if (n === 1)
+        return sortedValues[0];
+    const rank = (p / 100) * (n - 1);
+    const lo = Math.floor(rank);
+    const hi = Math.ceil(rank);
+    if (lo === hi)
+        return sortedValues[lo];
+    return sortedValues[lo] + (rank - lo) * (sortedValues[hi] - sortedValues[lo]);
+}
+/**
+ * Population standard deviation: sqrt(Σ(v − mean)² / n).
+ */
+function populationStddev(values, mean) {
+    const variance = values.reduce((acc, v) => acc + (v - mean) ** 2, 0) / values.length;
+    return Math.sqrt(variance);
+}
+/**
+ * Dispatch the computation for a single NumericPrimitive over the given rows/values.
+ * rows are ordered by t_start ASC from getObservations.
+ * values[i] === rows[i].value.
+ * Returns null only for zscore (n<2) and slope (degenerate denominator).
+ *
+ * The exhaustive switch + never guard ensures every new member of the union
+ * causes a compile-time error if not handled (ADR-3 code-review gate).
+ */
+function computePrimitive(primitive, rows, values, percentile) {
+    const n = values.length;
+    switch (primitive) {
+        case "mean": {
+            const sum = values.reduce((acc, v) => acc + v, 0);
+            return sum / n;
+        }
+        case "min":
+            return Math.min(...values);
+        case "max":
+            return Math.max(...values);
+        case "latest":
+            // rows are ordered t_start ASC; last element is the most recent.
+            return values[n - 1];
+        case "delta":
+            // latest − earliest (ASC order: first is earliest, last is latest).
+            return values[n - 1] - values[0];
+        case "slope":
+            return leastSquaresSlope(rows);
+        case "percentile": {
+            const sorted = [...values].sort((a, b) => a - b);
+            return linearPercentile(sorted, percentile);
+        }
+        case "zscore": {
+            if (n < 2)
+                return null; // population stddev undefined for n<2
+            const mean = values.reduce((acc, v) => acc + v, 0) / n;
+            const std = populationStddev(values, mean);
+            if (std === 0)
+                return 0; // all values identical → z-score is 0 by definition
+            const latest = values[n - 1];
+            return (latest - mean) / std;
+        }
+        default: {
+            // Exhaustive never guard: if a new primitive is added to the union without
+            // a case here, TypeScript will raise a compile error (ADR-3).
+            const _exhaustive = primitive;
+            throw new Error(`Unhandled NumericPrimitive: ${String(_exhaustive)}`);
+        }
+    }
+}
+// ── NumericsQueryLayer ────────────────────────────────────────────────
+/**
+ * Provides deterministic, LLM-free numeric aggregations over HealthDataStore.
+ *
+ * All methods are SYNCHRONOUS. No async, no fs, no network, no LLM import.
+ * The LLM never performs arithmetic — this layer does.
+ */
+export class NumericsQueryLayer {
+    store;
+    constructor(store) {
+        this.store = store;
+    }
+    /**
+     * Compute a numeric primitive over the observations in the given time window.
+     *
+     * Abstain conditions (return { value: null, sampleCount: 0 } without throwing):
+     *   - Empty window (no rows in the time range) — sc-4-6
+     *   - Heterogeneous units across rows — sc-4-7 (cross-unit refusal)
+     *
+     * Partial abstain (value: null, sampleCount: n):
+     *   - zscore with sampleCount < 2 (stddev undefined)
+     *   - slope with degenerate denominator (all same timestamp)
+     *
+     * @param window   — metric + ISO-8601 time range
+     * @param primitive — one of the 8 whitelisted NumericPrimitive values
+     * @param percentile — percentile p ∈ [0,100], used only for "percentile" primitive (default 50)
+     */
+    getMetric(window, primitive, percentile = 50) {
+        const rows = this.store.getObservations(window.metric, window.fromIso, window.toIso);
+        // ABSTAIN: empty window (sc-4-6)
+        if (rows.length === 0) {
+            return { primitive, value: null, unit: window.unit ?? "", sampleCount: 0 };
+        }
+        // UNIT GUARD (sc-4-7): refuse to aggregate across heterogeneous units (ADR-4).
+        // Architecture risk table line 328: "NumericsQueryLayer reads unit per row;
+        // refuses cross-unit aggregation."
+        const units = new Set(rows.map((r) => r.unit));
+        if (units.size > 1) {
+            // Abstain — no throw (no-throw contract from architecture API table line 251).
+            return { primitive, value: null, unit: "", sampleCount: rows.length };
+        }
+        const unit = rows[0].unit;
+        const values = rows.map((r) => r.value);
+        const value = computePrimitive(primitive, rows, values, percentile);
+        return { primitive, value, unit, sampleCount: rows.length };
+    }
+    /**
+     * Build a LabTrend summary for a biomarker series.
+     *
+     * Abstains (latestValue: null, slope: null) when sampleCount === 0 (sc-4-6).
+     * slope is null when sampleCount < 2 (not enough data for least-squares).
+     */
+    getLabTrend(biomarker) {
+        const series = this.store.getLabSeries(biomarker);
+        if (series.length === 0) {
+            return {
+                biomarker,
+                sampleCount: 0,
+                latestValue: null,
+                latestUnit: "",
+                latestCollectedAt: null,
+                slope: null,
+            };
+        }
+        // series is ordered collected_at ASC from getLabSeries.
+        const latest = series[series.length - 1];
+        let slope = null;
+        if (series.length >= 2) {
+            // Convert LabResult to pseudo-HealthObservation for slope helper reuse.
+            const pseudoRows = series.map((r) => ({
+                metric: r.biomarker,
+                value: r.value,
+                unit: r.unit,
+                tStart: r.collectedAtIso,
+                source: "lab",
+            }));
+            slope = leastSquaresSlope(pseudoRows);
+        }
+        return {
+            biomarker,
+            sampleCount: series.length,
+            latestValue: latest.value,
+            latestUnit: latest.unit,
+            latestCollectedAt: latest.collectedAtIso,
+            slope,
+        };
+    }
+}
+//# sourceMappingURL=numerics.js.map

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package/dist/medical/red-flag.d.ts

@@ -0,0 +1,42 @@
+/**
+ * RedFlagDetector — pure, synchronous, 0-LLM emergency detection (Phase 6, Sprint 3).
+ *
+ * ADR-2: Detection is deterministic and local. A conservative keyword/phrase match
+ * favors escalation reliability over paraphrase coverage. Novel phrasing may return
+ * 'none' and proceed to the normal (still-guardrailed) path — this is the accepted risk
+ * documented in ADR-2. Pattern set is versioned for auditability.
+ *
+ * NO async. NO fs. NO network. NO LLM import. Identical input => identical output.
+ */
+/** Six mutually-exclusive categories; 'none' means no emergency pattern matched. */
+export type RedFlagCategory = "cardiac" | "stroke" | "anaphylaxis" | "self-harm" | "overdose" | "none";
+/** Result of a single RedFlagDetector.detect() call. */
+export interface RedFlagMatch {
+    category: RedFlagCategory;
+    /**
+     * Rule ID that fired (IDs only — never prompt text).
+     * Undefined when category === 'none'.
+     */
+    ruleId?: string;
+}
+/** Versioned pattern-set identifier recorded in the audit log (ADR-2). */
+export declare const PATTERNSET_VERSION = "redflag-2026.06.16";
+/**
+ * Detects emergency red-flag phrases in a medical prompt.
+ *
+ * PURE + SYNCHRONOUS. No async, no fs, no network, no LLM import.
+ * Identical input => identical RedFlagMatch (asserted by sc-3-5).
+ *
+ * bober: conservative phrase matching; novel or indirect phrasing may return
+ *        'none' and fall through to normal SOP handling (ADR-2 accepted risk).
+ */
+export declare class RedFlagDetector {
+    readonly patternsetVersion = "redflag-2026.06.16";
+    /**
+     * Returns the first matching RedFlagMatch, or { category: 'none' } if no
+     * rule fires. Evaluation order is self-harm → overdose → cardiac → stroke →
+     * anaphylaxis so the correct emergency hotline (988 vs 911) is assigned.
+     */
+    detect(prompt: string): RedFlagMatch;
+}
+//# sourceMappingURL=red-flag.d.ts.map

package/dist/medical/red-flag.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/red-flag.js

@@ -0,0 +1,161 @@
+/**
+ * RedFlagDetector — pure, synchronous, 0-LLM emergency detection (Phase 6, Sprint 3).
+ *
+ * ADR-2: Detection is deterministic and local. A conservative keyword/phrase match
+ * favors escalation reliability over paraphrase coverage. Novel phrasing may return
+ * 'none' and proceed to the normal (still-guardrailed) path — this is the accepted risk
+ * documented in ADR-2. Pattern set is versioned for auditability.
+ *
+ * NO async. NO fs. NO network. NO LLM import. Identical input => identical output.
+ */
+// ── Version constant ─────────────────────────────────────────────────
+/** Versioned pattern-set identifier recorded in the audit log (ADR-2). */
+export const PATTERNSET_VERSION = "redflag-2026.06.16";
+/**
+ * Conservative rule list. Order matters:
+ * self-harm and overdose are checked so the correct hotline (988) wins over
+ * any incidental cardiac/anaphylaxis phrase in the same message.
+ *
+ * bober: phrase-include matching for now; upgrade to word-boundary regex or
+ *        an embedded trie if the pattern count grows to > 50 rules.
+ */
+const RULES = [
+    // ── self-harm (988) ──────────────────────────────────────────────
+    {
+        ruleId: "self-harm-suicidal",
+        category: "self-harm",
+        test: (n) => n.includes("suicidal") || n.includes("suicid"),
+    },
+    {
+        ruleId: "self-harm-kill-self",
+        category: "self-harm",
+        test: (n) => n.includes("kill myself") ||
+            n.includes("end my life") ||
+            n.includes("take my life") ||
+            n.includes("want to die"),
+    },
+    {
+        ruleId: "self-harm-self-harm",
+        category: "self-harm",
+        test: (n) => n.includes("hurt myself") || n.includes("harm myself"),
+    },
+    // ── overdose (988) ───────────────────────────────────────────────
+    {
+        ruleId: "overdose-explicit",
+        category: "overdose",
+        test: (n) => n.includes("overdose") || n.includes("over dose"),
+    },
+    {
+        ruleId: "overdose-too-many",
+        category: "overdose",
+        test: (n) => n.includes("took too many") || n.includes("taken too many"),
+    },
+    // ── cardiac (911) ────────────────────────────────────────────────
+    {
+        ruleId: "cardiac-chest-pain-radiating",
+        category: "cardiac",
+        test: (n) => n.includes("chest pain") && (n.includes("radiating") || n.includes("left arm")),
+    },
+    {
+        ruleId: "cardiac-chest-pain-breath",
+        category: "cardiac",
+        test: (n) => n.includes("chest pain") && (n.includes("short of breath") || n.includes("shortness of breath")),
+    },
+    {
+        ruleId: "cardiac-chest-crushing",
+        category: "cardiac",
+        test: (n) => (n.includes("crushing chest") || n.includes("chest pressure") || n.includes("chest tightness")) &&
+            (n.includes("arm") || n.includes("jaw") || n.includes("breath")),
+    },
+    {
+        ruleId: "cardiac-heart-attack",
+        category: "cardiac",
+        test: (n) => n.includes("heart attack"),
+    },
+    // ── stroke (911) — FAST: Face, Arms, Speech, Time ───────────────
+    {
+        ruleId: "stroke-face-droop",
+        category: "stroke",
+        test: (n) => n.includes("face droop") ||
+            n.includes("facial droop") ||
+            n.includes("drooping face"),
+    },
+    {
+        ruleId: "stroke-slurred-speech",
+        category: "stroke",
+        test: (n) => n.includes("slurred speech") ||
+            n.includes("slurring words") ||
+            n.includes("can't speak") ||
+            n.includes("cannot speak"),
+    },
+    {
+        ruleId: "stroke-arm-weakness",
+        category: "stroke",
+        test: (n) => (n.includes("arm weakness") || n.includes("arm numb")) &&
+            (n.includes("sudden") || n.includes("both arms")),
+    },
+    {
+        ruleId: "stroke-sudden-numbness",
+        category: "stroke",
+        test: (n) => n.includes("sudden numbness") || n.includes("sudden weakness"),
+    },
+    {
+        ruleId: "stroke-sudden-severe-headache",
+        category: "stroke",
+        test: (n) => n.includes("worst headache") ||
+            (n.includes("sudden") && n.includes("severe headache")),
+    },
+    // ── anaphylaxis (911) ────────────────────────────────────────────
+    {
+        ruleId: "anaphylaxis-throat-closing",
+        category: "anaphylaxis",
+        test: (n) => n.includes("throat closing") ||
+            n.includes("throat is closing") ||
+            n.includes("throat swelling"),
+    },
+    {
+        ruleId: "anaphylaxis-trouble-breathing-allergic",
+        category: "anaphylaxis",
+        test: (n) => n.includes("trouble breathing") &&
+            (n.includes("allergic") || n.includes("allergy") || n.includes("sting") || n.includes("peanut")),
+    },
+    {
+        ruleId: "anaphylaxis-cant-breathe-allergic",
+        category: "anaphylaxis",
+        test: (n) => (n.includes("can't breathe") || n.includes("cannot breathe")) &&
+            (n.includes("allergic") || n.includes("allergy") || n.includes("sting") || n.includes("peanut")),
+    },
+    {
+        ruleId: "anaphylaxis-anaphylaxis",
+        category: "anaphylaxis",
+        test: (n) => n.includes("anaphylaxis") || n.includes("anaphylactic"),
+    },
+];
+// ── RedFlagDetector ──────────────────────────────────────────────────
+/**
+ * Detects emergency red-flag phrases in a medical prompt.
+ *
+ * PURE + SYNCHRONOUS. No async, no fs, no network, no LLM import.
+ * Identical input => identical RedFlagMatch (asserted by sc-3-5).
+ *
+ * bober: conservative phrase matching; novel or indirect phrasing may return
+ *        'none' and fall through to normal SOP handling (ADR-2 accepted risk).
+ */
+export class RedFlagDetector {
+    patternsetVersion = PATTERNSET_VERSION;
+    /**
+     * Returns the first matching RedFlagMatch, or { category: 'none' } if no
+     * rule fires. Evaluation order is self-harm → overdose → cardiac → stroke →
+     * anaphylaxis so the correct emergency hotline (988 vs 911) is assigned.
+     */
+    detect(prompt) {
+        const norm = prompt.toLowerCase().trim();
+        for (const rule of RULES) {
+            if (rule.test(norm)) {
+                return { category: rule.category, ruleId: rule.ruleId };
+            }
+        }
+        return { category: "none" };
+    }
+}
+//# sourceMappingURL=red-flag.js.map

package/dist/medical/red-flag.js.map

@@ -0,0 +1 @@
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package/dist/medical/refusal.d.ts

@@ -0,0 +1,46 @@
+/**
+ * RefusalDetector — pure, synchronous, 0-LLM non-emergency content-policy refusal.
+ *
+ * Classifies prescription / specific-dosing / individualized-treatment-plan requests.
+ * Conservative phrase matching: accept FALSE-NEGATIVES (fall through to 'none'),
+ * NEVER false-positive into giving medical advice. Pattern set is versioned for audit.
+ *
+ * NO async. NO fs. NO network. NO LLM import. Identical input => identical output.
+ */
+/** Four mutually-exclusive categories; 'none' means no refusal pattern matched. */
+export type RefusalCategory = "prescription" | "specific-dosing" | "individualized-treatment-plan" | "none";
+/** Result of a single RefusalDetector.detect() call. */
+export interface RefusalMatch {
+    category: RefusalCategory;
+    /**
+     * Rule ID that fired (IDs only — never prompt text).
+     * Undefined when category === 'none'.
+     */
+    ruleId?: string;
+}
+/** Versioned pattern-set identifier recorded in the audit log. */
+export declare const REFUSAL_PATTERNSET_VERSION = "refusal-2026.06.17";
+/**
+ * Fixed canned reason strings per refusal category.
+ * Exported so callers can assert byte-equality (proving non-model-generation).
+ */
+export declare const REFUSAL_REASONS: Record<Exclude<RefusalCategory, "none">, string>;
+/**
+ * Detects non-emergency content-policy refusal phrases in a medical prompt.
+ *
+ * PURE + SYNCHRONOUS. No async, no fs, no network, no LLM import.
+ * Identical input => identical RefusalMatch output.
+ *
+ * bober: conservative phrase matching; novel or indirect phrasing may return
+ *        'none' and fall through to normal SOP handling (accepted risk; false-negative
+ *        is safer than false-positive into refused advice).
+ */
+export declare class RefusalDetector {
+    readonly patternsetVersion = "refusal-2026.06.17";
+    /**
+     * Returns the first matching RefusalMatch, or { category: 'none' } if no
+     * rule fires. Evaluation order is prescription → specific-dosing → treatment-plan.
+     */
+    detect(prompt: string): RefusalMatch;
+}
+//# sourceMappingURL=refusal.d.ts.map

package/dist/medical/refusal.d.ts.map

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