heor-agent-mcp 1.4.1 → 1.4.2

package/dist/data/niceTaPrecedents.d.ts

@@ -69,4 +69,5 @@ export interface PrecedentMismatch {
 }
 export declare function detectMismatch(drug: string, indication: string, userSuppliedTaNumber: string | null | undefined): PrecedentMismatch | null;
 export declare function extractTaNumber(text: string): string | null;
+export declare function extractAllTaNumbers(text: string): string[];
 //# sourceMappingURL=niceTaPrecedents.d.ts.map

package/dist/data/niceTaPrecedents.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"niceTaPrecedents.d.ts","sourceRoot":"","sources":["../../src/data/niceTaPrecedents.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,MAAM,CAAC;IACb,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,GAAG,QAAQ,CAAC;CAC/B;AAED;;;;;GAKG;AACH,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,aAAa,CAuEnD,CAAC;AAEF;;;;;;;;;GASG;AACH,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,GACjB,aAAa,EAAE,CAkBjB;AAED;;;;;;;;;GASG;AACH,MAAM,WAAW,iBAAiB;IAChC,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,EAClB,oBAAoB,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAC9C,iBAAiB,GAAG,IAAI,CAiC1B;AAQD,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG3D"}
+{"version":3,"file":"niceTaPrecedents.d.ts","sourceRoot":"","sources":["../../src/data/niceTaPrecedents.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,MAAM,CAAC;IACb,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,GAAG,QAAQ,CAAC;CAC/B;AAED;;;;;GAKG;AACH,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,aAAa,CAiGnD,CAAC;AAEF;;;;;;;;;GASG;AACH,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,GACjB,aAAa,EAAE,CA+BjB;AAED;;;;;;;;;GASG;AACH,MAAM,WAAW,iBAAiB;IAChC,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,aAAa,EAAE,MAAM,CAAC;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,EAClB,oBAAoB,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAC9C,iBAAiB,GAAG,IAAI,CAiC1B;AAYD,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG3D;AAQD,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAY1D"}

package/dist/data/niceTaPrecedents.js

@@ -10,7 +10,11 @@ export const PRECEDENTS = [
     {
         ta_number: "TA679",
         drug: "dapagliflozin",
-        indication_keywords: ["hfref", "heart failure with reduced ejection fraction", "reduced ejection fraction"],
+        indication_keywords: [
+            "hfref",
+            "heart failure with reduced ejection fraction",
+            "reduced ejection fraction",
+        ],
         title: "Dapagliflozin for treating chronic heart failure with reduced ejection fraction",
         date: "2021-02",
         url: "https://www.nice.org.uk/guidance/ta679",
@@ -20,7 +24,12 @@ export const PRECEDENTS = [
     {
         ta_number: "TA902",
         drug: "dapagliflozin",
-        indication_keywords: ["hfpef", "hfmref", "preserved ejection fraction", "mildly reduced ejection fraction"],
+        indication_keywords: [
+            "hfpef",
+            "hfmref",
+            "preserved ejection fraction",
+            "mildly reduced ejection fraction",
+        ],
         title: "Dapagliflozin for treating chronic heart failure with preserved or mildly reduced ejection fraction",
         date: "2023-06",
         url: "https://www.nice.org.uk/guidance/ta902",
@@ -30,7 +39,10 @@ export const PRECEDENTS = [
     {
         ta_number: "TA773",
         drug: "empagliflozin",
-        indication_keywords: ["hfref", "heart failure with reduced ejection fraction"],
+        indication_keywords: [
+            "hfref",
+            "heart failure with reduced ejection fraction",
+        ],
         title: "Empagliflozin for treating chronic heart failure with reduced ejection fraction",
         date: "2022-03",
         url: "https://www.nice.org.uk/guidance/ta773",
@@ -39,7 +51,12 @@ export const PRECEDENTS = [
     {
         ta_number: "TA929",
         drug: "empagliflozin",
-        indication_keywords: ["hfpef", "hfmref", "preserved ejection fraction", "mildly reduced ejection fraction"],
+        indication_keywords: [
+            "hfpef",
+            "hfmref",
+            "preserved ejection fraction",
+            "mildly reduced ejection fraction",
+        ],
         title: "Empagliflozin for treating chronic heart failure with preserved or mildly reduced ejection fraction",
         date: "2023-09",
         url: "https://www.nice.org.uk/guidance/ta929",
@@ -69,7 +86,11 @@ export const PRECEDENTS = [
     {
         ta_number: "TA388",
         drug: "sacubitril valsartan",
-        indication_keywords: ["heart failure", "hfref", "reduced ejection fraction"],
+        indication_keywords: [
+            "heart failure",
+            "hfref",
+            "reduced ejection fraction",
+        ],
         title: "Sacubitril valsartan for treating symptomatic chronic heart failure with reduced ejection fraction",
         date: "2016-04",
         url: "https://www.nice.org.uk/guidance/ta388",
@@ -91,8 +112,19 @@ export function findPrecedents(drug, indication) {
     const indicationLower = indication.toLowerCase().trim();
     if (!drugLower || !indicationLower)
         return [];
+    // Token-set drug match: split both sides on whitespace AND hyphen
+    // ("sacubitril-valsartan" ↔ "sacubitril valsartan"), then require the
+    // two token sets to be EQUAL. Prevents false positives like single-word
+    // "valsartan" (ARB) matching multi-word "sacubitril valsartan" (ARNI).
+    // Bare "valsartan" → set {valsartan} ≠ {sacubitril, valsartan} → no match.
+    // "sacubitril valsartan" → set {sacubitril, valsartan} = {sacubitril,
+    // valsartan} → match.
+    const tokenize = (s) => new Set(s.split(/[\s-]+/).filter(Boolean));
+    const drugTokens = tokenize(drugLower);
     const scored = PRECEDENTS.map((p) => {
-        const drugMatch = drugLower.includes(p.drug) || p.drug.includes(drugLower);
+        const pTokens = tokenize(p.drug);
+        const drugMatch = drugTokens.size === pTokens.size &&
+            [...drugTokens].every((w) => pTokens.has(w));
         if (!drugMatch)
             return { p, score: 0 };
         const matchedKeywords = p.indication_keywords.filter((kw) => indicationLower.includes(kw));
@@ -143,10 +175,33 @@ export function detectMismatch(drug, indication, userSuppliedTaNumber) {
  * Extract a TA number (e.g. "TA902") from arbitrary prose. Returns
  * the first match or null. Used to scan e.g. evidence_summary for
  * a TA number the user may have referenced informally.
+ *
+ * Handles common prose variations: "TA679", "TA 679", "NICE TA 773",
+ * "TA679." (with trailing punctuation). Output is normalised to
+ * "TA<digits>" form (no internal whitespace).
  */
-const TA_NUMBER_REGEX = /\b(TA\d{2,4})\b/i;
+const TA_NUMBER_REGEX = /\bTA\s*(\d{2,4})\b/i;
 export function extractTaNumber(text) {
     const m = text.match(TA_NUMBER_REGEX);
-    return m ? m[1].toUpperCase() : null;
+    return m ? `TA${m[1]}` : null;
+}
+/**
+ * Extract ALL TA numbers from arbitrary prose (not just the first).
+ * Useful when an evidence summary references multiple appraisals
+ * (e.g. "Per TA902 for HFpEF and TA679 for HFrEF").
+ */
+const TA_NUMBER_REGEX_GLOBAL = /\bTA\s*(\d{2,4})\b/gi;
+export function extractAllTaNumbers(text) {
+    const matches = Array.from(text.matchAll(TA_NUMBER_REGEX_GLOBAL));
+    const seen = new Set();
+    const out = [];
+    for (const m of matches) {
+        const norm = `TA${m[1]}`;
+        if (!seen.has(norm)) {
+            seen.add(norm);
+            out.push(norm);
+        }
+    }
+    return out;
 }
 //# sourceMappingURL=niceTaPrecedents.js.map

package/dist/data/niceTaPrecedents.js.map

@@ -1 +1 @@
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package/dist/jca/countryRegistry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"countryRegistry.d.ts","sourceRoot":"","sources":["../../src/jca/countryRegistry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,KAAK,EAEV,cAAc,EAEd,kBAAkB,EAClB,YAAY,EAEZ,eAAe,EAChB,MAAM,YAAY,CAAC;AAEpB,eAAO,MAAM,YAAY,EAAG,SAAkB,CAAC;AAyT/C,eAAO,MAAM,gBAAgB,EAAE,MAAM,CAAC,YAAY,EAAE,cAAc,CAoBjE,CAAC;AAEF;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,UAAU,EAAE,MAAM,GAAG,kBAAkB,CA6EzE;AAED,wBAAgB,UAAU,CAAC,YAAY,EAAE,YAAY,GAAG,cAAc,CAErE;AAED,wBAAgB,0BAA0B,CACxC,QAAQ,EAAE,kBAAkB,GAC3B,eAAe,EAAE,CAEnB"}
+{"version":3,"file":"countryRegistry.d.ts","sourceRoot":"","sources":["../../src/jca/countryRegistry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AACH,OAAO,KAAK,EAEV,cAAc,EAEd,kBAAkB,EAClB,YAAY,EAEZ,eAAe,EAChB,MAAM,YAAY,CAAC;AAEpB,eAAO,MAAM,YAAY,EAAG,SAAkB,CAAC;AA+U/C,eAAO,MAAM,gBAAgB,EAAE,MAAM,CAAC,YAAY,EAAE,cAAc,CAoBjE,CAAC;AAEF;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,UAAU,EAAE,MAAM,GAAG,kBAAkB,CA6EzE;AAED,wBAAgB,UAAU,CAAC,YAAY,EAAE,YAAY,GAAG,cAAc,CAErE;AAED,wBAAgB,0BAA0B,CACxC,QAAQ,EAAE,kBAAkB,GAC3B,eAAe,EAAE,CAEnB"}

package/dist/jca/countryRegistry.js

@@ -9,6 +9,11 @@ function instrumentsFor(category) {
     if (category === "diabetes_t2" || category === "obesity") {
         return ["EQ-5D-5L", "IWQOL-Lite"];
     }
+    if (category === "cardiovascular_hfref") {
+        // KCCQ-12 is the disease-specific HRQoL instrument used in DAPA-HF
+        // and EMPEROR-Reduced and required by EUnetHTA Annex II for HFrEF.
+        return ["KCCQ-12", "EQ-5D-5L"];
+    }
     return ["EQ-5D-5L"];
 }
 function oncologyOutcomePriority() {
@@ -21,11 +26,17 @@ function chronicOutcomePriority() {
     return ["HRQoL", "remission", "AE", "other"];
 }
 function hfrefOutcomePriority() {
-    // EuroQol Annex II preference + DAPA-HF / EMPEROR-Reduced primary
-    // composite. CV death and HF hospitalization sit at the top of the
-    // patient-relevant outcomes hierarchy for HFrEF; HRQoL via KCCQ/EQ-5D
-    // is a key secondary.
+    // DAPA-HF and EMPEROR-Reduced both used "CV death OR HF hospitalization"
+    // as a SINGLE co-primary composite endpoint, not two independent ranked
+    // outcomes. EUnetHTA Annex II accepts this composite as the primary
+    // patient-relevant outcome for HFrEF. We list the composite first so the
+    // tool output doesn't imply a hierarchy regulators reject. Component
+    // outcomes (CV_death, HF_hospitalization) follow for transparency.
+    // all_cause_mortality is reported but logically subsumes CV_death; it's
+    // listed below the components rather than between them to avoid the
+    // contradiction the prior order produced.
     return [
+        "CV_death_or_HF_hospitalization",
         "CV_death",
         "HF_hospitalization",
         "all_cause_mortality",
@@ -221,8 +232,9 @@ function cardiovascularHfrefComparators(country) {
         ];
     }
     if (country === "uk") {
-        // Post-Brexit context only — NICE TA679 already established empagliflozin
-        // as a relevant in-class comparator; SoC includes ARNI per NG106.
+        // Post-Brexit context only — NICE TA773 (empagliflozin HFrEF, March 2022)
+        // and TA679 (dapagliflozin HFrEF, Feb 2021) already established the SGLT2i
+        // class as relevant in-class comparators; SoC includes ARNI per NG106.
         return [gdmtArni, empa];
     }
     // eu_other or unknown — degrade gracefully
@@ -281,6 +293,16 @@ function subgroupsFor(category) {
     if (category === "obesity") {
         return ["BMI category", "comorbidities (T2D, CV, OSA)"];
     }
+    if (category === "cardiovascular_hfref") {
+        return [
+            "NYHA class (II vs III-IV)",
+            "LVEF stratum (≤35% vs 35-40%)",
+            "background GDMT completeness (ACEi/ARB/ARNI + beta-blocker + MRA)",
+            "ARNI eligibility (ESC 2021)",
+            "eGFR tier (renal impairment)",
+            "diabetes status (T2D yes/no)",
+        ];
+    }
     return ["age strata", "comorbidity status"];
 }
 function profile(jurisdiction, hta_body) {

package/dist/jca/countryRegistry.js.map

@@ -1 +1 @@
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package/dist/jca/scopeEligibility.d.ts

@@ -2,7 +2,7 @@
  * EU JCA scope eligibility checker.
  *
  * Per Regulation (EU) 2021/2282, JCA scope is phased:
- *   • From 12 January 2025: oncology medicinal products + ATMPs with
+ *   • From 13 January 2025: oncology medicinal products + ATMPs with
  *     new active substances.
  *   • From 13 January 2028: orphan medicinal products added.
  *   • From 13 January 2030: all new medicinal products.

package/dist/jca/scopeEligibility.js

@@ -13,7 +13,7 @@ export function checkScopeEligibility(args) {
         "EU Implementing Regulation 2024/1381 — JCA procedural rules.",
         "European Commission factsheet, JCA for Medicinal Products (Jan 2025): https://health.ec.europa.eu/document/download/ced91156-ffe1-472d-85eb-aa6a91dd707e_en?filename=hta_htar_factsheet-jca_en.pdf",
     ];
-    // Phase 1 (in scope NOW, since 12 Jan 2025): oncology medicinal
+    // Phase 1 (in scope NOW, since 13 Jan 2025): oncology medicinal
     // products + ATMP-class drugs (cell, gene, tissue) with new
     // active substances.
     const isOncology = args.indication_category === "oncology_nsclc" ||
@@ -26,7 +26,7 @@ export function checkScopeEligibility(args) {
             in_scope: true,
             in_scope_from_year: 2025,
             phase: "oncology_atmp",
-            explanation: "In JCA scope since 12 January 2025 (Phase 1: oncology medicinal products + ATMPs with new active substances).",
+            explanation: "In JCA scope since 13 January 2025 (Phase 1: oncology medicinal products + ATMPs with new active substances).",
             references: refs,
         };
     }

package/dist/jca/types.d.ts

@@ -1,7 +1,7 @@
 export type Jurisdiction = "de" | "fr" | "it" | "es" | "nl" | "uk" | "eu_other";
 export type DrugClass = "monoclonal_antibody" | "small_molecule" | "atmp_cell" | "atmp_gene" | "atmp_tissue" | "biosimilar" | "vaccine" | "radiopharmaceutical" | "other";
 export type LineOfTherapy = "first_line" | "second_line" | "third_line_plus" | "any";
-export type OutcomePriority = "OS" | "PFS" | "HRQoL" | "AE" | "remission" | "CV_death" | "HF_hospitalization" | "all_cause_mortality" | "NYHA_progression" | "other";
+export type OutcomePriority = "OS" | "PFS" | "HRQoL" | "AE" | "remission" | "CV_death_or_HF_hospitalization" | "CV_death" | "HF_hospitalization" | "all_cause_mortality" | "NYHA_progression" | "other";
 export interface ComparatorEntry {
     molecule: string;
     rationale: string;

package/dist/jca/types.d.ts.map

@@ -1 +1 @@
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package/dist/tools/htaWorkflow.d.ts

@@ -158,8 +158,8 @@ export declare const htaWorkflowToolSchema: {
         readonly title: "HTA Submission Workflow Orchestrator";
         readonly readOnlyHint: true;
         readonly destructiveHint: false;
-        readonly idempotentHint: true;
-        readonly openWorldHint: false;
+        readonly idempotentHint: false;
+        readonly openWorldHint: true;
     };
     readonly inputSchema: {
         readonly type: "object";

package/dist/tools/htaWorkflow.d.ts.map

@@ -1 +1 @@
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package/dist/tools/htaWorkflow.js

@@ -25,7 +25,15 @@ 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";
-const HTA_BODIES = ["nice", "ema", "fda", "iqwig", "has", "jca", "gvd"];
+const HTA_BODIES = [
+    "nice",
+    "ema",
+    "fda",
+    "iqwig",
+    "has",
+    "jca",
+    "gvd",
+];
 const SUBMISSION_TYPES = [
     "sta",
     "mta",
@@ -189,6 +197,14 @@ export async function runHtaWorkflow(rawInput, deps) {
     const input = parsed.data;
     let audit = createAuditRecord("hta.workflow", input, "text");
     audit = setMethodology(audit, "End-to-end HTA submission pipeline: literature_search (runs=N for stability) → screen_abstracts (PICO) → risk_of_bias (RoB 2 / ROBINS-I / AMSTAR-2 auto-instrument) → cost_effectiveness_model (Markov/PartSA + PSA) → hta_dossier (auto-GRADE from RoB output) → validate_links (post-hoc URL audit). Each phase wrapped in safe-run so single-step failures do not abort the pipeline.");
+    // JCA-route guard: when hta_body="jca", this orchestrator runs the
+    // standard pipeline without calling jca_pico_scope, so the JCA scope
+    // eligibility check (Reg 2021/2282 phased rollout) does NOT fire.
+    // Surface this so an out-of-scope indication can't silently produce
+    // a credible-looking JCA dossier.
+    if (input.hta_body === "jca") {
+        audit = addWarning(audit, "hta_body='jca' — this orchestrator does NOT run jca_pico_scope, so the JCA scope eligibility check (Reg 2021/2282: oncology+ATMP from 13 Jan 2025; orphans from 13 Jan 2028; all medicines from 13 Jan 2030) is bypassed. Verify the indication is actually in JCA scope before treating this output as submission-grade. To check scope explicitly, call jca_pico_scope first.");
+    }
     const t0 = Date.now();
     const phaseTimings = {};
     // ── Phase 1: literature_search ─────────────────────────────────────
@@ -225,10 +241,35 @@ export async function runHtaWorkflow(rawInput, deps) {
             output_format: "json",
         }));
         if (screenRes.ok) {
+            // CRITICAL FIX (v1.4.2 code review): screen_abstracts JSON output
+            // returns ScreeningResult objects that LACK the `abstract` field.
+            // If we passed those straight through to risk_of_bias, RoB
+            // inference would silently run on empty abstracts and return
+            // "Unclear" for every domain — corrupting GRADE downstream.
+            //
+            // Instead: extract the included/uncertain IDs from the screening
+            // result and re-map them onto the ORIGINAL literatureRecords
+            // (which still carry the abstract text).
             const screened = extractLiteratureResults(screenRes.value);
-            if (screened.length > 0) {
-                screenedRecords = screened;
-                audit = addAssumption(audit, `Phase 2 (screen_abstracts) included ${screened.length} of ${literatureRecords.length} records via PICO filter.`);
+            const includedIds = new Set(screened
+                .filter((r) => {
+                const status = r
+                    .screening_status;
+                return !status || status === "include" || status === "uncertain";
+            })
+                .map((r) => String(r.id ?? ""))
+                .filter(Boolean));
+            const remapped = includedIds.size > 0
+                ? literatureRecords.filter((r) => includedIds.has(String(r.id ?? "")))
+                : [];
+            if (remapped.length > 0) {
+                screenedRecords = remapped;
+                audit = addAssumption(audit, `Phase 2 (screen_abstracts) included ${remapped.length} of ${literatureRecords.length} records via PICO filter; abstracts preserved for downstream RoB inference.`);
+            }
+            else if (screened.length > 0) {
+                // Screening returned results but none mapped back to original IDs.
+                // Fall back to the unfiltered set with abstracts intact and warn.
+                audit = addWarning(audit, `Phase 2 (screen_abstracts) returned ${screened.length} screened records but none could be re-mapped to original literature IDs (likely an ID-shape mismatch). Falling back to unfiltered ${literatureRecords.length} records with abstracts preserved.`);
             }
             else {
                 // Fallback: if screener returns 0, keep the unfiltered set with a warning.
@@ -297,8 +338,7 @@ export async function runHtaWorkflow(rawInput, deps) {
                 ae_cost: ce.ae_cost ?? 0,
                 admin_cost: ce.admin_cost ?? 0,
             },
-            utility_inputs: ce.qaly_on_treatment !== undefined ||
-                ce.qaly_comparator !== undefined
+            utility_inputs: ce.qaly_on_treatment !== undefined || ce.qaly_comparator !== undefined
                 ? {
                     qaly_on_treatment: ce.qaly_on_treatment,
                     qaly_comparator: ce.qaly_comparator,
@@ -339,7 +379,13 @@ export async function runHtaWorkflow(rawInput, deps) {
     else {
         audit = addAssumption(audit, `Phase 4 (cost_effectiveness_model) skipped (skip_ce_model=true).`);
     }
-    phaseTimings.cost_effectiveness_model = Date.now() - tCe;
+    // Only record CE timing when CE actually ran. Setting it to a small
+    // non-zero on the skip path made `phase_timings_ms.cost_effectiveness_model`
+    // a misleading proxy for "did CE run?" and caused the skip-path test to
+    // be flaky on slower CI.
+    if (!input.skip_ce_model) {
+        phaseTimings.cost_effectiveness_model = Date.now() - tCe;
+    }
     // ── Phase 5: hta_dossier ──────────────────────────────────────────
     const tDossier = Date.now();
     const dossierRes = await safeRun(() => deps.htaDossier({
@@ -422,7 +468,9 @@ export async function runHtaWorkflow(rawInput, deps) {
     else {
         lines.push(`| 4 | cost_effectiveness_model | ${phaseTimings.cost_effectiveness_model ?? 0} | ${ceSummaryText || (ceResults ? "ran" : "failed")} |`);
     }
-    lines.push(`| 5 | hta_dossier | ${phaseTimings.hta_dossier ?? 0} | ${input.hta_body.toUpperCase()} ${input.submission_type.toUpperCase()} draft |`);
+    lines.push(`| 5 | hta_dossier | ${phaseTimings.hta_dossier ?? 0} | ${dossierRes.ok
+        ? `${input.hta_body.toUpperCase()} ${input.submission_type.toUpperCase()} draft`
+        : "FAILED — see audit"} |`);
     lines.push(`| 6 | validate_links | ${phaseTimings.validate_links ?? 0} | ${validationCounts.working}/${allUrls.length} working, ${validationCounts.broken} broken |`);
     lines.push("");
     // The dossier is the primary user-facing artifact.
@@ -481,8 +529,12 @@ export const htaWorkflowToolSchema = {
         title: "HTA Submission Workflow Orchestrator",
         readOnlyHint: true,
         destructiveHint: false,
-        idempotentHint: true,
-        openWorldHint: false,
+        // Stochastic Phase 4 PSA + live external API calls (PubMed,
+        // ClinicalTrials.gov, validate_links HTTP) make this NOT idempotent
+        // and definitively open-world. Caching by MCP clients on the
+        // idempotent hint would return stale CE estimates.
+        idempotentHint: false,
+        openWorldHint: true,
     },
     inputSchema: {
         type: "object",

package/dist/tools/htaWorkflow.js.map

@@ -1 +1 @@
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package/dist/tools/jcaPicoScope.d.ts

@@ -50,6 +50,15 @@ export declare const jcaPicoScopeToolSchema: {
                 readonly enum: readonly ["pre_authorisation", "post_authorisation", "conditional_approval"];
                 readonly default: "post_authorisation";
             };
+            readonly is_orphan: {
+                readonly type: "boolean";
+                readonly description: "Optional. Orphan-designated medicinal product. Affects JCA scope eligibility (orphans enter scope from 13 January 2028 vs 13 January 2030 for general medicinal products).";
+            };
+            readonly force_proceed_out_of_scope: {
+                readonly type: "boolean";
+                readonly default: false;
+                readonly description: "Override the JCA scope eligibility check. Default false. Set true to produce a JCA-style matrix anyway when the indication is not yet in JCA scope (e.g., for protocol-design or anticipatory market-access work). Output will carry an explicit out-of-scope warning either way.";
+            };
         };
         readonly required: readonly ["drug", "indication", "drug_class"];
     };

package/dist/tools/jcaPicoScope.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"jcaPicoScope.d.ts","sourceRoot":"","sources":["../../src/tools/jcaPicoScope.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAqDxD,wBAAsB,kBAAkB,CACtC,QAAQ,EAAE,OAAO,GAChB,OAAO,CAAC,UAAU,CAAC,CAuTrB;AAED,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgDzB,CAAC"}

package/dist/tools/jcaPicoScope.js

@@ -145,6 +145,16 @@ export async function handleJcaPicoScope(rawInput) {
         input.line_of_therapy !== "second_line") {
         audit = addWarning(audit, `NSCLC comparator detail (chemo doublet + IO + alternative TKI) is currently modeled only for line_of_therapy="second_line"; you passed "${input.line_of_therapy}", so the per-country EGFR-mutant detail was skipped and a generic chemotherapy anchor was used instead. Re-run with line_of_therapy="second_line" for the well-modeled case.`);
     }
+    // Heart-failure ambiguity warning: HFpEF and HFrEF have completely
+    // different comparator universes. When a user passes bare "heart
+    // failure" without an EF qualifier, classifyIndication routes to
+    // generic `cardiovascular` and serves placeholders. Surface this so
+    // the user re-runs with HFrEF / HFpEF / HFmrEF specified.
+    if (matrix.indication_category === "cardiovascular" &&
+        /heart\s*failure/i.test(input.indication) &&
+        !/reduced ejection|hfref|preserved ejection|hfpef|mildly reduced|hfmref/i.test(input.indication)) {
+        audit = addWarning(audit, `Indication "${input.indication}" is ambiguous: HFpEF, HFmrEF, and HFrEF have materially different comparator universes (e.g., SGLT2i + ARNI structure differs). Currently routing to generic cardiovascular placeholders. Re-run with the specific phenotype (e.g., "heart failure with reduced ejection fraction" / "HFrEF" / "HFpEF") for the well-modeled case.`);
+    }
     const lines = [];
     lines.push(`# JCA PICO Scope — ${input.drug} (${input.indication})`);
     lines.push("");
@@ -273,6 +283,15 @@ export const jcaPicoScopeToolSchema = {
                 enum: REG_CONTEXTS,
                 default: "post_authorisation",
             },
+            is_orphan: {
+                type: "boolean",
+                description: "Optional. Orphan-designated medicinal product. Affects JCA scope eligibility (orphans enter scope from 13 January 2028 vs 13 January 2030 for general medicinal products).",
+            },
+            force_proceed_out_of_scope: {
+                type: "boolean",
+                default: false,
+                description: "Override the JCA scope eligibility check. Default false. Set true to produce a JCA-style matrix anyway when the indication is not yet in JCA scope (e.g., for protocol-design or anticipatory market-access work). Output will carry an explicit out-of-scope warning either way.",
+            },
         },
         required: ["drug", "indication", "drug_class"],
     },

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "heor-agent-mcp",
-  "version": "1.4.1",
+  "version": "1.4.2",
   "mcpName": "io.github.neptun2000/heor-agent",
   "license": "MIT",
   "author": "mnaumov",