heor-agent-mcp 1.2.2 → 1.3.2

package/dist/tools/pvSignalWorkflow.js

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+/**
+ * pv_signal_workflow — EMA GVP Module IX rev 2 signal management.
+ *
+ * Given drug-AE case counts from EudraVigilance / FAERS / national PV
+ * databases, compute disproportionality statistics (PRR, ROR, IC, MGPS),
+ * decide a signal verdict, and emit canonical RMP signal-section text.
+ *
+ * Pure logic, no I/O. Pairs with pv_classify (planned-study classifier).
+ * See design log #14.
+ */
+import { z } from "zod";
+import { addAssumption, addWarning, createAuditRecord, setMethodology, } from "../audit/builder.js";
+import { auditToMarkdown } from "../formatters/markdown.js";
+import { suggestForEnum } from "../util/didYouMean.js";
+import { computeAllStats, decideVerdict } from "../pv/signalDecision.js";
+import { GVP_REVISION } from "../pv/gvpModules.js";
+const DATA_SOURCES = [
+    "eudravigilance",
+    "faers",
+    "vigibase_who",
+    "national_db",
+    "spontaneous_internal",
+];
+const PvSignalWorkflowSchema = z
+    .object({
+    drug: z.string().min(1, "drug is required"),
+    indication: z.string().min(1, "indication is required"),
+    reporting_period_months: z.number().int().min(1).max(120).default(12),
+    case_counts: z
+        .object({
+        drug_event: z.number().int().nonnegative(),
+        drug_total: z.number().int().nonnegative(),
+        event_total: z.number().int().nonnegative(),
+        grand_total: z.number().int().nonnegative(),
+    })
+        .refine((d) => d.drug_total >= d.drug_event, {
+        message: "drug_total must be >= drug_event (cell b = drug_total - drug_event would be negative)",
+    })
+        .refine((d) => d.event_total >= d.drug_event, {
+        message: "event_total must be >= drug_event (cell c = event_total - drug_event would be negative)",
+    })
+        .refine((d) => d.grand_total >= d.drug_total + (d.event_total - d.drug_event), {
+        message: "grand_total too small — cell d = grand_total - drug_total - (event_total - drug_event) would be negative. Check that all 4 counts come from the same database.",
+    }),
+    data_source: z.enum(DATA_SOURCES).default("eudravigilance"),
+    pregnancy_exposure: z.boolean().default(false),
+    prior_known_signals: z.array(z.string()).default([]),
+    reported_event: z
+        .string()
+        .optional()
+        .describe("Optional: the specific adverse event being scored (e.g., 'lactic acidosis'). REQUIRED to enable previously_known_signal classification — without it, the tool cannot determine whether the disproportionality applies to a known event vs a new one. When omitted with prior_known_signals non-empty, output emits a warning and treats the case as a potentially new signal."),
+    outcome_serious: z.boolean().default(false),
+    rmp_has_pregnancy_concern: z.boolean().default(false),
+})
+    .strict();
+export async function handlePvSignalWorkflow(rawInput) {
+    const parsed = PvSignalWorkflowSchema.safeParse(rawInput);
+    if (!parsed.success) {
+        const messages = [];
+        for (const issue of parsed.error.issues) {
+            if (issue.code === "invalid_enum_value" &&
+                typeof issue.received === "string") {
+                const suggestions = suggestForEnum(issue.received, issue.options);
+                messages.push(`Invalid ${issue.path.join(".")}: "${issue.received}". Allowed: ${issue.options.join(", ")}.${suggestions.length
+                    ? ` Did you mean ${suggestions.map((s) => `"${s}"`).join(", ")}?`
+                    : ""}`);
+            }
+            else {
+                messages.push(`${issue.path.join(".") || "input"}: ${issue.message}`);
+            }
+        }
+        throw new Error(messages.join("\n"));
+    }
+    const input = parsed.data;
+    let audit = createAuditRecord("pv.signal_workflow", input, "text");
+    audit = setMethodology(audit, "EMA GVP Module IX rev 2 (Signal management); EU Implementing Reg. 2025/1466 (mandatory EVDAS integration from 2026-02-12); Evans 2001 (PRR); van Puijenbroek 2002 (ROR); Bate 1998 / Norén 2006 (IC, BCPNN); DuMouchel 1999 (MGPS, EBGM, gamma-Poisson shrinkage). GVP Considerations P.III for pregnancy follow-up gating.");
+    const stats = computeAllStats(input.case_counts, input.outcome_serious);
+    const verdict = decideVerdict({
+        stats,
+        prior_known_signals: input.prior_known_signals,
+        reported_event: input.reported_event,
+        outcome_serious: input.outcome_serious,
+    });
+    // Honest-API guard: when caller has prior_known_signals but didn't supply
+    // reported_event, we cannot match the disproportionality to a specific
+    // known signal. Surface this in the audit so reviewers see we treated it
+    // as a potentially new signal rather than silently suppressing it.
+    if (input.prior_known_signals.length > 0 &&
+        !input.reported_event &&
+        [
+            stats.prr.threshold_met,
+            stats.ror.threshold_met,
+            stats.ic.threshold_met,
+            stats.mgps.threshold_met,
+        ].filter(Boolean).length >= 2) {
+        audit = addWarning(audit, "prior_known_signals supplied but reported_event missing — cannot match to a specific known signal. Verdict treats this as a potentially new signal. Re-run with reported_event to enable previously_known_signal classification.");
+    }
+    audit = addAssumption(audit, `${stats.thresholds_used} thresholds applied. ${[
+        stats.prr.threshold_met,
+        stats.ror.threshold_met,
+        stats.ic.threshold_met,
+        stats.mgps.threshold_met,
+    ].filter(Boolean).length}/4 methods triggered.`);
+    if (verdict === "confirmed_signal") {
+        audit = addWarning(audit, `Confirmed signal — recommend PRAC notification, RMP signal-section update, ICSR review.`);
+    }
+    const wantsPregnancyFollowup = input.pregnancy_exposure && input.rmp_has_pregnancy_concern;
+    const pregnancy_followup = wantsPregnancyFollowup
+        ? {
+            timepoints: ["birth", "3_months", "12_months"],
+            followup_protocol_ref: "GVP-P.III-2026",
+            structured_data_required: [
+                "pregnancy outcome (live birth / spontaneous abortion / elective TOP / stillbirth)",
+                "gestational age at exposure",
+                "gestational age at delivery",
+                "birth weight + length + head circumference",
+                "congenital anomalies (any organ system, classified by ICD-10)",
+                "developmental milestones at 3 months and 12 months",
+                "breastfeeding status at follow-up timepoints",
+            ],
+        }
+        : undefined;
+    const recommendations = recommendationsFor(verdict, stats, input);
+    const rmpText = rmpSignalSectionText(input, stats, verdict);
+    const signal_assessment = {
+        drug: input.drug,
+        period_months: input.reporting_period_months,
+        statistics: {
+            prr: stats.prr,
+            ror: stats.ror,
+            ic: stats.ic,
+            mgps: stats.mgps,
+            chi_squared: stats.chi_squared,
+            n_cases: stats.n_cases,
+        },
+        verdict,
+        workflow_recommendation: recommendations,
+        rmp_signal_section_text: rmpText,
+        pregnancy_followup,
+        gvp_revision: GVP_REVISION,
+    };
+    // ── Markdown report ─────────────────────────────────────────────────────
+    const lines = [];
+    lines.push(`# PV Signal Assessment — ${input.drug} (${input.indication})`);
+    lines.push("");
+    lines.push(`**Data source:** ${input.data_source} · **Period:** ${input.reporting_period_months} months · **N cases:** ${stats.n_cases} · **Threshold tier:** ${stats.thresholds_used}`);
+    lines.push("");
+    lines.push(`**Verdict:** \`${verdict}\``);
+    lines.push("");
+    lines.push("## Disproportionality statistics");
+    lines.push("| Method | Value | 95% CI / posterior | Threshold met? |");
+    lines.push("|--------|-------|--------------------|----------------|");
+    lines.push(`| PRR (Evans 2001) | ${stats.prr.value.toFixed(2)} | [${stats.prr.ci_low.toFixed(2)}, ${stats.prr.ci_high.toFixed(2)}] | ${stats.prr.threshold_met ? "✅" : "❌"} |`);
+    lines.push(`| ROR (van Puijenbroek 2002) | ${stats.ror.value.toFixed(2)} | [${stats.ror.ci_low.toFixed(2)}, ${stats.ror.ci_high.toFixed(2)}] | ${stats.ror.threshold_met ? "✅" : "❌"} |`);
+    lines.push(`| IC (BCPNN, Bate 1998) | ${stats.ic.value.toFixed(2)} | IC025 = ${stats.ic.ic025.toFixed(2)} | ${stats.ic.threshold_met ? "✅" : "❌"} |`);
+    lines.push(`| MGPS / EBGM (DuMouchel 1999) | ${stats.mgps.ebgm.toFixed(2)} | EB05 = ${stats.mgps.eb05.toFixed(2)} · EB95 = ${stats.mgps.eb95.toFixed(2)} | ${stats.mgps.threshold_met ? "✅" : "❌"} |`);
+    lines.push(`| χ² (Yates) | ${stats.chi_squared.toFixed(2)} | — | ${stats.chi_squared >= 4 ? "✅" : "❌"} |`);
+    lines.push("");
+    lines.push("## Workflow recommendation");
+    for (const r of recommendations)
+        lines.push(`- ${r}`);
+    lines.push("");
+    if (pregnancy_followup) {
+        lines.push("## GVP Considerations P.III — Pregnancy follow-up");
+        lines.push("The drug has a pregnancy-related safety concern in the RMP and pregnancy exposure was reported. Per GVP Considerations P.III (effective 2026-02-09), structured follow-up is required at:");
+        lines.push("");
+        for (const t of pregnancy_followup.timepoints)
+            lines.push(`- **${t}**`);
+        lines.push("");
+        lines.push(`Structured data to capture (protocol ref \`${pregnancy_followup.followup_protocol_ref}\`):`);
+        for (const d of pregnancy_followup.structured_data_required)
+            lines.push(`- ${d}`);
+        lines.push("");
+    }
+    else if (input.pregnancy_exposure) {
+        lines.push("## Pregnancy exposure noted");
+        lines.push("Pregnancy exposure was reported but `rmp_has_pregnancy_concern: false` — per GVP Considerations P.III, structured follow-up is required *in principle only when the medicinal product is associated with pregnancy-related safety concerns identified in the RMP*. Confirm RMP status; if a pregnancy-related risk is in scope, re-run with `rmp_has_pregnancy_concern: true`.");
+        lines.push("");
+    }
+    lines.push("## RMP signal-section text (canonical)");
+    lines.push("```");
+    lines.push(rmpText);
+    lines.push("```");
+    lines.push("");
+    lines.push("## Roadmap notes");
+    lines.push("- **v2 (planned):** EVDAS programmatic integration via eRMR / ICSR download per Reg. 2025/1466 — currently this tool takes user-supplied case counts.");
+    lines.push("- **v2 (planned):** Stratified MGPS (by sex / age band) — currently single-stratum gamma-Poisson shrinkage.");
+    lines.push("");
+    lines.push("## References");
+    lines.push("- EMA GVP Module IX rev 2 (Signal management, 2026)");
+    lines.push("- EU Implementing Regulation 2025/1466 (mandatory EVDAS integration)");
+    lines.push("- EMA GVP Considerations P.III — Pregnancy and breastfeeding");
+    lines.push("- Evans SJW et al. (2001). PRR for signal generation. *PDS* 10:483-486.");
+    lines.push("- van Puijenbroek EP et al. (2002). ROR for signal detection. *PDS* 11:3-10.");
+    lines.push("- Bate A et al. (1998). BCPNN signal detection. *Eur J Clin Pharmacol* 54:315-321.");
+    lines.push("- Norén GN et al. (2006). Extending IC to bivariate cases. *Stat Med* 25:1995-2017.");
+    lines.push("- DuMouchel W. (1999). Bayesian data mining in large freq tables. *Am Stat* 53:177-190.");
+    lines.push("");
+    lines.push(auditToMarkdown(audit));
+    return {
+        content: lines.join("\n"),
+        audit,
+        signal_assessment,
+    };
+}
+function recommendationsFor(verdict, stats, input) {
+    const out = [];
+    switch (verdict) {
+        case "confirmed_signal":
+            out.push("Notify PRAC within the next signal management cycle.");
+            out.push("Update RMP Part III (PV Plan) with the new signal section text below.");
+            out.push("Conduct ICSR-level review of the contributing cases.");
+            out.push("Consider whether a label variation is warranted; if yes, file Type II variation.");
+            if (input.outcome_serious) {
+                out.push("⚠️ AE is serious — accelerated review timeline applies (lower thresholds were used).");
+            }
+            break;
+        case "strengthening_signal":
+            out.push("Continue monitoring; re-evaluate at next PSUR cycle.");
+            out.push("Document in signal management tracking system; not yet a confirmed signal.");
+            out.push(`Currently ${[stats.prr.threshold_met, stats.ror.threshold_met, stats.ic.threshold_met, stats.mgps.threshold_met].filter(Boolean).length}/4 methods trigger; needs ≥2 + N≥3 + χ²≥4 for confirmation.`);
+            break;
+        case "previously_known_signal":
+            out.push("Signal matches a previously-identified known risk in the RMP.");
+            out.push("Confirm continued reporting in the next PSUR; no new RMP variation required.");
+            break;
+        case "refuted_signal":
+            out.push("Statistics significantly below threshold with adequate N.");
+            out.push("Document non-signal in signal management tracking; no further action required.");
+            break;
+        case "no_signal":
+        default:
+            out.push("No disproportionality detected. Continue routine PV monitoring.");
+            out.push("Re-evaluate at next PSUR cycle or if N grows materially.");
+    }
+    if (input.pregnancy_exposure && input.rmp_has_pregnancy_concern) {
+        out.push("GVP P.III follow-up required (birth / 3mo / 12mo) — see protocol below.");
+    }
+    return out;
+}
+function rmpSignalSectionText(input, stats, verdict) {
+    return [
+        `Signal: ${input.drug} in ${input.indication}.`,
+        `Source: ${input.data_source}, ${input.reporting_period_months}-month reporting period.`,
+        `Cases (N): ${stats.n_cases}.`,
+        `PRR = ${stats.prr.value.toFixed(2)} (95% CI ${stats.prr.ci_low.toFixed(2)}-${stats.prr.ci_high.toFixed(2)}); ROR = ${stats.ror.value.toFixed(2)} (95% CI ${stats.ror.ci_low.toFixed(2)}-${stats.ror.ci_high.toFixed(2)}); IC = ${stats.ic.value.toFixed(2)} (IC025 = ${stats.ic.ic025.toFixed(2)}); EBGM = ${stats.mgps.ebgm.toFixed(2)} (EB05 = ${stats.mgps.eb05.toFixed(2)}); χ² = ${stats.chi_squared.toFixed(2)}.`,
+        `Verdict: ${verdict.replace(/_/g, " ")}.`,
+        `Threshold tier: ${stats.thresholds_used}.`,
+    ].join(" ");
+}
+export const pvSignalWorkflowToolSchema = {
+    name: "pv.signal_workflow",
+    description: "Compute disproportionality statistics (PRR, ROR, IC/BCPNN, MGPS/EBGM) on user-supplied drug-AE case counts and decide a signal verdict per EMA GVP Module IX rev 2. Returns the verdict (no/strengthening/confirmed/previously known/refuted), workflow recommendations, and canonical RMP signal-section text. To classify a finding as previously_known_signal, supply BOTH prior_known_signals AND reported_event so the tool can match the disproportionality to a specific known event. Optionally layers in GVP Considerations P.III pregnancy follow-up (birth/3mo/12mo) when both pregnancy_exposure and rmp_has_pregnancy_concern are true. Pairs with pv_classify. ⚠️ MGPS uses single-stratum gamma-Poisson shrinkage in v1 — when database counts are confounded by sex/age strata, EBGM/EB05 may be inflated; stratified MGPS is planned for v2. v1 takes user counts; v2 will also integrate EVDAS programmatic access per Reg. 2025/1466.",
+    annotations: {
+        title: "PV Signal Workflow",
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+    inputSchema: {
+        type: "object",
+        properties: {
+            drug: { type: "string" },
+            indication: { type: "string" },
+            reporting_period_months: {
+                type: "number",
+                minimum: 1,
+                maximum: 120,
+                default: 12,
+            },
+            case_counts: {
+                type: "object",
+                properties: {
+                    drug_event: {
+                        type: "number",
+                        minimum: 0,
+                        description: "a — cases of THIS drug AND THIS event",
+                    },
+                    drug_total: {
+                        type: "number",
+                        minimum: 0,
+                        description: "a+b — all cases of the drug",
+                    },
+                    event_total: {
+                        type: "number",
+                        minimum: 0,
+                        description: "a+c — all cases of the event",
+                    },
+                    grand_total: {
+                        type: "number",
+                        minimum: 0,
+                        description: "a+b+c+d — all cases in DB",
+                    },
+                },
+                required: ["drug_event", "drug_total", "event_total", "grand_total"],
+            },
+            data_source: {
+                type: "string",
+                enum: DATA_SOURCES,
+                default: "eudravigilance",
+            },
+            pregnancy_exposure: { type: "boolean", default: false },
+            prior_known_signals: {
+                type: "array",
+                items: { type: "string" },
+                default: [],
+            },
+            outcome_serious: { type: "boolean", default: false },
+            rmp_has_pregnancy_concern: { type: "boolean", default: false },
+        },
+        required: ["drug", "indication", "case_counts"],
+    },
+};
+//# sourceMappingURL=pvSignalWorkflow.js.map

package/dist/tools/pvSignalWorkflow.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "heor-agent-mcp",
-  "version": "1.2.2",
+  "version": "1.3.2",
   "mcpName": "io.github.neptun2000/heor-agent",
   "license": "MIT",
   "author": "mnaumov",