heor-agent-mcp 1.3.2 → 1.4.0

package/dist/server.js

@@ -27,6 +27,7 @@ import { handleUtilityValueSet, utilityValueSetToolSchema, } from "./tools/utili
 import { handleItcFeasibility, itcFeasibilityToolSchema, } from "./tools/itcFeasibility.js";
 import { handleExamples, examplesToolSchema } from "./tools/examples.js";
 import { handleMaicWorkflow, maicWorkflowToolSchema, } from "./tools/maicWorkflow.js";
+import { handleHtaWorkflow, htaWorkflowToolSchema, } from "./tools/htaWorkflow.js";
 import { handlePvClassify, pvClassifyToolSchema } from "./tools/pvClassify.js";
 import { handleJcaPicoScope, jcaPicoScopeToolSchema, } from "./tools/jcaPicoScope.js";
 import { handlePvSignalWorkflow, pvSignalWorkflowToolSchema, } from "./tools/pvSignalWorkflow.js";
@@ -164,6 +165,7 @@ function createMcpServer(surfaceRef = { value: "direct_mcp" }, sessionIdRef = {
             pvClassifyToolSchema,
             jcaPicoScopeToolSchema,
             pvSignalWorkflowToolSchema,
+            htaWorkflowToolSchema,
         ],
     }));
     server.setRequestHandler(CallToolRequestSchema, async (request) => {
@@ -238,6 +240,9 @@ function createMcpServer(surfaceRef = { value: "direct_mcp" }, sessionIdRef = {
                 case "pv.signal_workflow":
                     result = await handlePvSignalWorkflow(args);
                     break;
+                case "hta.workflow":
+                    result = await handleHtaWorkflow(args);
+                    break;
                 default:
                     trackToolCall(name, Date.now() - callStart, "error", sessionIdRef.value || undefined, {
                         surface: surfaceRef.value,

package/dist/server.js.map

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

@@ -0,0 +1,299 @@
+/**
+ * hta_workflow — server-side orchestrator that runs the canonical
+ * HTA submission pipeline in a single MCP call. Built because generic
+ * LLMs (ChatGPT, Claude.ai, Copilot) require 4-5 separate prompts +
+ * manual context re-paste to chain literature_search → screen_abstracts
+ * → risk_of_bias → cost_effectiveness_model → hta_dossier → validate_links.
+ * This tool absorbs the orchestration burden so a single prompt produces
+ * the full dossier package.
+ *
+ * Pipeline (5 phases):
+ *   Phase 1 (sequential): literature_search (runs=N for stability)
+ *   Phase 2 (sequential): screen_abstracts on PICO criteria
+ *   Phase 3 (sequential): risk_of_bias on screened set
+ *   Phase 4 (sequential): cost_effectiveness_model with indication-derived defaults
+ *   Phase 5 (sequential): hta_dossier consuming evidence + rob + model outputs
+ *   Phase 6 (sequential): validate_links on every URL cited across the run
+ *
+ * Each phase is wrapped in safeRun so a single failure doesn't kill the
+ * whole pipeline — the report shows which phase ran, which fell back,
+ * and what to do next.
+ *
+ * See design log #17.
+ */
+import { z } from "zod";
+import type { ToolResult } from "../providers/types.js";
+declare const HtaWorkflowSchema: z.ZodObject<{
+    drug: z.ZodString;
+    indication: z.ZodString;
+    hta_body: z.ZodDefault<z.ZodEnum<["nice", "ema", "fda", "iqwig", "has", "jca", "gvd"]>>;
+    submission_type: z.ZodDefault<z.ZodEnum<["sta", "mta", "early_access", "initial", "renewal", "variation"]>>;
+    perspective: z.ZodDefault<z.ZodEnum<["nhs", "us_payer", "societal"]>>;
+    drug_class: z.ZodDefault<z.ZodEnum<["monoclonal_antibody", "small_molecule", "atmp_cell", "atmp_gene", "atmp_tissue", "biosimilar", "vaccine", "radiopharmaceutical", "other"]>>;
+    is_orphan: z.ZodDefault<z.ZodBoolean>;
+    pico: z.ZodOptional<z.ZodObject<{
+        population: z.ZodOptional<z.ZodString>;
+        intervention: z.ZodOptional<z.ZodString>;
+        comparator: z.ZodOptional<z.ZodString>;
+        outcomes: z.ZodOptional<z.ZodArray<z.ZodString, "many">>;
+    }, "strip", z.ZodTypeAny, {
+        population?: string | undefined;
+        intervention?: string | undefined;
+        comparator?: string | undefined;
+        outcomes?: string[] | undefined;
+    }, {
+        population?: string | undefined;
+        intervention?: string | undefined;
+        comparator?: string | undefined;
+        outcomes?: string[] | undefined;
+    }>>;
+    ce_inputs: z.ZodOptional<z.ZodObject<{
+        drug_cost_annual: z.ZodOptional<z.ZodNumber>;
+        comparator_cost_annual: z.ZodOptional<z.ZodNumber>;
+        efficacy_delta: z.ZodOptional<z.ZodNumber>;
+        ae_cost: z.ZodOptional<z.ZodNumber>;
+        admin_cost: z.ZodOptional<z.ZodNumber>;
+        qaly_on_treatment: z.ZodOptional<z.ZodNumber>;
+        qaly_comparator: z.ZodOptional<z.ZodNumber>;
+    }, "strip", z.ZodTypeAny, {
+        efficacy_delta?: number | undefined;
+        drug_cost_annual?: number | undefined;
+        comparator_cost_annual?: number | undefined;
+        qaly_on_treatment?: number | undefined;
+        qaly_comparator?: number | undefined;
+        admin_cost?: number | undefined;
+        ae_cost?: number | undefined;
+    }, {
+        efficacy_delta?: number | undefined;
+        drug_cost_annual?: number | undefined;
+        comparator_cost_annual?: number | undefined;
+        qaly_on_treatment?: number | undefined;
+        qaly_comparator?: number | undefined;
+        admin_cost?: number | undefined;
+        ae_cost?: number | undefined;
+    }>>;
+    sources: z.ZodDefault<z.ZodArray<z.ZodEnum<["pubmed", "clinicaltrials", "biorxiv", "cochrane", "nice_ta", "cadth_reviews", "icer_reports", "ispor", "wiley"]>, "many">>;
+    max_literature_results: z.ZodDefault<z.ZodNumber>;
+    literature_runs: z.ZodDefault<z.ZodNumber>;
+    jurisdictions: z.ZodDefault<z.ZodArray<z.ZodEnum<["de", "fr", "it", "es", "nl", "uk", "eu_other"]>, "many">>;
+    skip_ce_model: z.ZodDefault<z.ZodBoolean>;
+}, "strict", z.ZodTypeAny, {
+    hta_body: "nice" | "ema" | "fda" | "iqwig" | "has" | "jca" | "gvd";
+    submission_type: "sta" | "mta" | "early_access" | "initial" | "renewal" | "variation";
+    drug: string;
+    indication: string;
+    sources: ("pubmed" | "clinicaltrials" | "biorxiv" | "cochrane" | "nice_ta" | "cadth_reviews" | "icer_reports" | "ispor" | "wiley")[];
+    perspective: "nhs" | "us_payer" | "societal";
+    drug_class: "other" | "monoclonal_antibody" | "small_molecule" | "atmp_cell" | "atmp_gene" | "atmp_tissue" | "biosimilar" | "vaccine" | "radiopharmaceutical";
+    is_orphan: boolean;
+    max_literature_results: number;
+    literature_runs: number;
+    jurisdictions: ("de" | "fr" | "it" | "es" | "nl" | "uk" | "eu_other")[];
+    skip_ce_model: boolean;
+    pico?: {
+        population?: string | undefined;
+        intervention?: string | undefined;
+        comparator?: string | undefined;
+        outcomes?: string[] | undefined;
+    } | undefined;
+    ce_inputs?: {
+        efficacy_delta?: number | undefined;
+        drug_cost_annual?: number | undefined;
+        comparator_cost_annual?: number | undefined;
+        qaly_on_treatment?: number | undefined;
+        qaly_comparator?: number | undefined;
+        admin_cost?: number | undefined;
+        ae_cost?: number | undefined;
+    } | undefined;
+}, {
+    drug: string;
+    indication: string;
+    hta_body?: "nice" | "ema" | "fda" | "iqwig" | "has" | "jca" | "gvd" | undefined;
+    submission_type?: "sta" | "mta" | "early_access" | "initial" | "renewal" | "variation" | undefined;
+    sources?: ("pubmed" | "clinicaltrials" | "biorxiv" | "cochrane" | "nice_ta" | "cadth_reviews" | "icer_reports" | "ispor" | "wiley")[] | undefined;
+    perspective?: "nhs" | "us_payer" | "societal" | undefined;
+    pico?: {
+        population?: string | undefined;
+        intervention?: string | undefined;
+        comparator?: string | undefined;
+        outcomes?: string[] | undefined;
+    } | undefined;
+    drug_class?: "other" | "monoclonal_antibody" | "small_molecule" | "atmp_cell" | "atmp_gene" | "atmp_tissue" | "biosimilar" | "vaccine" | "radiopharmaceutical" | undefined;
+    is_orphan?: boolean | undefined;
+    ce_inputs?: {
+        efficacy_delta?: number | undefined;
+        drug_cost_annual?: number | undefined;
+        comparator_cost_annual?: number | undefined;
+        qaly_on_treatment?: number | undefined;
+        qaly_comparator?: number | undefined;
+        admin_cost?: number | undefined;
+        ae_cost?: number | undefined;
+    } | undefined;
+    max_literature_results?: number | undefined;
+    literature_runs?: number | undefined;
+    jurisdictions?: ("de" | "fr" | "it" | "es" | "nl" | "uk" | "eu_other")[] | undefined;
+    skip_ce_model?: boolean | undefined;
+}>;
+export type HtaWorkflowInput = z.infer<typeof HtaWorkflowSchema>;
+type Handler = (args: unknown) => Promise<unknown>;
+export interface HtaWorkflowDeps {
+    literatureSearch: Handler;
+    screenAbstracts: Handler;
+    riskOfBias: Handler;
+    costEffectivenessModel: Handler;
+    htaDossier: Handler;
+    validateLinks: Handler;
+    jcaPicoScope?: Handler;
+}
+export declare function runHtaWorkflow(rawInput: unknown, deps: HtaWorkflowDeps): Promise<ToolResult>;
+/**
+ * Production handler — wraps runHtaWorkflow with the real tool handlers
+ * imported lazily to avoid circular dependencies.
+ */
+export declare function handleHtaWorkflow(rawInput: unknown): Promise<ToolResult>;
+export declare const htaWorkflowToolSchema: {
+    readonly name: "hta.workflow";
+    readonly description: "End-to-end HTA submission orchestrator. One call runs literature_search (with PRISMA-style stability via runs=N) → screen_abstracts (PICO filter) → risk_of_bias (auto RoB 2/ROBINS-I/AMSTAR-2) → cost_effectiveness_model (Markov + 1k PSA, defaults from indication) → hta_dossier (auto-GRADE downgrade from RoB output) → validate_links (post-hoc URL audit). Returns a combined report with per-phase timings, the full dossier draft, and the URL validation table. Use as a single-shot drop-in replacement for the 4-5 separate prompts a generic LLM would need to chain these tools manually. Each phase wrapped in safe-run so single-step failures do not abort the pipeline.";
+    readonly annotations: {
+        readonly title: "HTA Submission Workflow Orchestrator";
+        readonly readOnlyHint: true;
+        readonly destructiveHint: false;
+        readonly idempotentHint: true;
+        readonly openWorldHint: false;
+    };
+    readonly inputSchema: {
+        readonly type: "object";
+        readonly properties: {
+            readonly drug: {
+                readonly type: "string";
+                readonly description: "Drug or intervention name.";
+            };
+            readonly indication: {
+                readonly type: "string";
+                readonly description: "Disease or condition (free text).";
+            };
+            readonly hta_body: {
+                readonly type: "string";
+                readonly enum: readonly ["nice", "ema", "fda", "iqwig", "has", "jca", "gvd"];
+                readonly default: "nice";
+                readonly description: "Target HTA body for the dossier draft.";
+            };
+            readonly submission_type: {
+                readonly type: "string";
+                readonly enum: readonly ["sta", "mta", "early_access", "initial", "renewal", "variation"];
+                readonly default: "sta";
+            };
+            readonly perspective: {
+                readonly type: "string";
+                readonly enum: readonly ["nhs", "us_payer", "societal"];
+                readonly default: "nhs";
+                readonly description: "Economic perspective for the cost-effectiveness model phase.";
+            };
+            readonly drug_class: {
+                readonly type: "string";
+                readonly enum: readonly ["monoclonal_antibody", "small_molecule", "atmp_cell", "atmp_gene", "atmp_tissue", "biosimilar", "vaccine", "radiopharmaceutical", "other"];
+                readonly default: "small_molecule";
+            };
+            readonly is_orphan: {
+                readonly type: "boolean";
+                readonly default: false;
+                readonly description: "Orphan-designated medicinal product. Affects JCA scope eligibility (orphans enter JCA scope 2028 vs 2030 for general medicinal products).";
+            };
+            readonly pico: {
+                readonly type: "object";
+                readonly properties: {
+                    readonly population: {
+                        readonly type: "string";
+                    };
+                    readonly intervention: {
+                        readonly type: "string";
+                    };
+                    readonly comparator: {
+                        readonly type: "string";
+                    };
+                    readonly outcomes: {
+                        readonly type: "array";
+                        readonly items: {
+                            readonly type: "string";
+                        };
+                    };
+                };
+                readonly description: "Optional PICO criteria for the screening phase (defaults derived from drug + indication).";
+            };
+            readonly ce_inputs: {
+                readonly type: "object";
+                readonly description: "Optional cost-effectiveness model inputs. Sensible defaults applied when omitted (efficacy_delta=0.25; drug_cost_annual=1000; SoC=0).";
+                readonly properties: {
+                    readonly drug_cost_annual: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                    };
+                    readonly comparator_cost_annual: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                    };
+                    readonly efficacy_delta: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                        readonly maximum: 1;
+                    };
+                    readonly ae_cost: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                    };
+                    readonly admin_cost: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                    };
+                    readonly qaly_on_treatment: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                        readonly maximum: 1;
+                    };
+                    readonly qaly_comparator: {
+                        readonly type: "number";
+                        readonly minimum: 0;
+                        readonly maximum: 1;
+                    };
+                };
+            };
+            readonly sources: {
+                readonly type: "array";
+                readonly items: {
+                    readonly type: "string";
+                    readonly enum: readonly ["pubmed", "clinicaltrials", "biorxiv", "cochrane", "nice_ta", "cadth_reviews", "icer_reports", "ispor", "wiley"];
+                };
+                readonly default: readonly ["pubmed", "clinicaltrials"];
+            };
+            readonly max_literature_results: {
+                readonly type: "number";
+                readonly minimum: 1;
+                readonly maximum: 100;
+                readonly default: 30;
+            };
+            readonly literature_runs: {
+                readonly type: "number";
+                readonly minimum: 1;
+                readonly maximum: 5;
+                readonly default: 3;
+                readonly description: "Number of dedup-stability passes for the literature_search phase. 3 is the project default for HTA-grade reproducibility.";
+            };
+            readonly jurisdictions: {
+                readonly type: "array";
+                readonly items: {
+                    readonly type: "string";
+                    readonly enum: readonly ["de", "fr", "it", "es", "nl", "uk", "eu_other"];
+                };
+                readonly default: readonly ["de", "fr", "it", "es", "nl"];
+            };
+            readonly skip_ce_model: {
+                readonly type: "boolean";
+                readonly default: false;
+                readonly description: "Skip the cost-effectiveness model phase (e.g., for clinical-only dossiers).";
+            };
+        };
+        readonly required: readonly ["drug", "indication"];
+    };
+};
+export {};
+//# sourceMappingURL=htaWorkflow.d.ts.map

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package/dist/tools/htaWorkflow.js

@@ -0,0 +1,580 @@
+/**
+ * hta_workflow — server-side orchestrator that runs the canonical
+ * HTA submission pipeline in a single MCP call. Built because generic
+ * LLMs (ChatGPT, Claude.ai, Copilot) require 4-5 separate prompts +
+ * manual context re-paste to chain literature_search → screen_abstracts
+ * → risk_of_bias → cost_effectiveness_model → hta_dossier → validate_links.
+ * This tool absorbs the orchestration burden so a single prompt produces
+ * the full dossier package.
+ *
+ * Pipeline (5 phases):
+ *   Phase 1 (sequential): literature_search (runs=N for stability)
+ *   Phase 2 (sequential): screen_abstracts on PICO criteria
+ *   Phase 3 (sequential): risk_of_bias on screened set
+ *   Phase 4 (sequential): cost_effectiveness_model with indication-derived defaults
+ *   Phase 5 (sequential): hta_dossier consuming evidence + rob + model outputs
+ *   Phase 6 (sequential): validate_links on every URL cited across the run
+ *
+ * Each phase is wrapped in safeRun so a single failure doesn't kill the
+ * whole pipeline — the report shows which phase ran, which fell back,
+ * and what to do next.
+ *
+ * See design log #17.
+ */
+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 SUBMISSION_TYPES = [
+    "sta",
+    "mta",
+    "early_access",
+    "initial",
+    "renewal",
+    "variation",
+];
+const PERSPECTIVES = ["nhs", "us_payer", "societal"];
+const DRUG_CLASSES = [
+    "monoclonal_antibody",
+    "small_molecule",
+    "atmp_cell",
+    "atmp_gene",
+    "atmp_tissue",
+    "biosimilar",
+    "vaccine",
+    "radiopharmaceutical",
+    "other",
+];
+const SOURCES = [
+    "pubmed",
+    "clinicaltrials",
+    "biorxiv",
+    "cochrane",
+    "nice_ta",
+    "cadth_reviews",
+    "icer_reports",
+    "ispor",
+    "wiley",
+];
+const HtaWorkflowSchema = z
+    .object({
+    drug: z.string().min(1, "drug is required"),
+    indication: z.string().min(1, "indication is required"),
+    hta_body: z.enum(HTA_BODIES).default("nice"),
+    submission_type: z.enum(SUBMISSION_TYPES).default("sta"),
+    perspective: z.enum(PERSPECTIVES).default("nhs"),
+    drug_class: z.enum(DRUG_CLASSES).default("small_molecule"),
+    is_orphan: z.boolean().default(false),
+    pico: z
+        .object({
+        population: z.string().optional(),
+        intervention: z.string().optional(),
+        comparator: z.string().optional(),
+        outcomes: z.array(z.string()).optional(),
+    })
+        .optional(),
+    ce_inputs: z
+        .object({
+        drug_cost_annual: z.number().min(0).optional(),
+        comparator_cost_annual: z.number().min(0).optional(),
+        efficacy_delta: z.number().min(0).max(1).optional(),
+        ae_cost: z.number().min(0).optional(),
+        admin_cost: z.number().min(0).optional(),
+        qaly_on_treatment: z.number().min(0).max(1).optional(),
+        qaly_comparator: z.number().min(0).max(1).optional(),
+    })
+        .optional(),
+    sources: z
+        .array(z.enum(SOURCES))
+        .min(1)
+        .default(["pubmed", "clinicaltrials"]),
+    max_literature_results: z.number().int().min(1).max(100).default(30),
+    literature_runs: z.number().int().min(1).max(5).default(3),
+    jurisdictions: z
+        .array(z.enum(["de", "fr", "it", "es", "nl", "uk", "eu_other"]))
+        .default(["de", "fr", "it", "es", "nl"]),
+    skip_ce_model: z
+        .boolean()
+        .default(false)
+        .describe("Skip the cost-effectiveness model phase (e.g., when the dossier is clinical-only)."),
+})
+    .strict();
+function isToolResult(x) {
+    return typeof x === "object" && x !== null && "content" in x;
+}
+function asText(x) {
+    if (!isToolResult(x))
+        return "";
+    return typeof x.content === "string"
+        ? x.content
+        : JSON.stringify(x.content, null, 2);
+}
+async function safeRun(fn) {
+    try {
+        return { ok: true, value: await fn() };
+    }
+    catch (e) {
+        return {
+            ok: false,
+            error: e instanceof Error ? e.message : String(e),
+        };
+    }
+}
+function isRecord(x) {
+    return typeof x === "object" && x !== null;
+}
+/**
+ * Extract literature records from a literature_search ToolResult that
+ * was called with output_format="json". The JSON-mode handler returns
+ * { content: <stringified JSON> } where the inner JSON has a `results`
+ * array. We robustly handle both shapes (object-content and string-content).
+ */
+function extractLiteratureResults(raw) {
+    if (!isRecord(raw))
+        return [];
+    const content = raw.content;
+    let parsed = content;
+    if (typeof content === "string") {
+        try {
+            parsed = JSON.parse(content);
+        }
+        catch {
+            return [];
+        }
+    }
+    if (!isRecord(parsed))
+        return [];
+    const results = parsed.results;
+    if (!Array.isArray(results))
+        return [];
+    return results.filter((r) => isRecord(r));
+}
+/**
+ * Extract URLs from the workflow's output content for the final
+ * link-validation phase. We scan a combined Markdown blob for
+ * https://… URL patterns. Deduplicates and caps at 50 (the
+ * validate_links limit).
+ */
+const URL_REGEX = /https?:\/\/[^\s)\]"'>]+/g;
+function extractUrls(text, cap = 50) {
+    const urls = new Set();
+    for (const m of text.matchAll(URL_REGEX)) {
+        // Strip trailing punctuation that's commonly attached in prose.
+        const u = m[0].replace(/[.,;:!?]+$/, "");
+        urls.add(u);
+        if (urls.size >= cap)
+            break;
+    }
+    return Array.from(urls);
+}
+export async function runHtaWorkflow(rawInput, deps) {
+    const parsed = HtaWorkflowSchema.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"}: ${issue.message}`);
+            }
+        }
+        throw new Error(messages.join("\n"));
+    }
+    const input = parsed.data;
+    let audit = createAuditRecord("hta.workflow", input, "text");
+    audit = setMethodology(audit, "End-to-end HTA submission pipeline: literature_search (runs=N for stability) → screen_abstracts (PICO) → risk_of_bias (RoB 2 / ROBINS-I / AMSTAR-2 auto-instrument) → cost_effectiveness_model (Markov/PartSA + PSA) → hta_dossier (auto-GRADE from RoB output) → validate_links (post-hoc URL audit). Each phase wrapped in safe-run so single-step failures do not abort the pipeline.");
+    const t0 = Date.now();
+    const phaseTimings = {};
+    // ── Phase 1: literature_search ─────────────────────────────────────
+    const tLit = Date.now();
+    const litQuery = `${input.drug} ${input.indication}`;
+    const litRes = await safeRun(() => deps.literatureSearch({
+        query: litQuery,
+        sources: input.sources,
+        max_results: input.max_literature_results,
+        runs: input.literature_runs,
+        output_format: "json",
+    }));
+    phaseTimings.literature_search = Date.now() - tLit;
+    let literatureRecords = [];
+    if (litRes.ok) {
+        literatureRecords = extractLiteratureResults(litRes.value);
+        audit = addAssumption(audit, `Phase 1 (literature_search) returned ${literatureRecords.length} records across ${input.sources.join(", ")} (${phaseTimings.literature_search}ms).`);
+    }
+    else {
+        audit = addWarning(audit, `Phase 1 (literature_search) failed: ${litRes.error}. Downstream phases will fall back to evidence_summary=null.`);
+    }
+    // ── Phase 2: screen_abstracts ─────────────────────────────────────
+    const tScreen = Date.now();
+    let screenedRecords = literatureRecords;
+    if (literatureRecords.length > 0) {
+        const screenRes = await safeRun(() => deps.screenAbstracts({
+            results: literatureRecords,
+            criteria: {
+                population: input.pico?.population ?? `adults with ${input.indication}`,
+                intervention: input.pico?.intervention ?? input.drug,
+                comparator: input.pico?.comparator,
+                outcomes: input.pico?.outcomes,
+            },
+            output_format: "json",
+        }));
+        if (screenRes.ok) {
+            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.`);
+            }
+            else {
+                // Fallback: if screener returns 0, keep the unfiltered set with a warning.
+                audit = addWarning(audit, `Phase 2 (screen_abstracts) returned 0 included records; falling back to unfiltered ${literatureRecords.length} records for downstream phases.`);
+            }
+        }
+        else {
+            audit = addWarning(audit, `Phase 2 (screen_abstracts) failed: ${screenRes.error}. Using unfiltered literature for downstream phases.`);
+        }
+    }
+    phaseTimings.screen_abstracts = Date.now() - tScreen;
+    // ── Phase 3: risk_of_bias ─────────────────────────────────────────
+    const tRob = Date.now();
+    let robResults = undefined;
+    let robSummaryText = "";
+    if (screenedRecords.length > 0) {
+        const robRes = await safeRun(() => deps.riskOfBias({
+            studies: screenedRecords.slice(0, 10), // Cap at top-10 for tractable RoB
+            instrument: "auto",
+            output_format: "json",
+        }));
+        if (robRes.ok) {
+            const robContent = robRes.value.content;
+            if (typeof robContent === "string") {
+                try {
+                    robResults = JSON.parse(robContent);
+                }
+                catch {
+                    robResults = robContent;
+                }
+            }
+            else {
+                robResults = robContent;
+            }
+            // Best-effort summary line
+            if (isRecord(robResults) &&
+                isRecord(robResults.summary)) {
+                const s = robResults.summary;
+                robSummaryText = `RoB summary: ${s.n_assessed ?? "?"} assessed; instruments: RoB 2 ×${s.rob2_count ?? 0}, ROBINS-I ×${s.robins_i_count ?? 0}, AMSTAR-2 ×${s.amstar2_count ?? 0}; overall judgement: ${s.rob_judgment ?? "n/a"}.`;
+            }
+            audit = addAssumption(audit, `Phase 3 (risk_of_bias) assessed ${screenedRecords.slice(0, 10).length} top-included studies.`);
+        }
+        else {
+            audit = addWarning(audit, `Phase 3 (risk_of_bias) failed: ${robRes.error}. hta_dossier GRADE will use heuristic estimates instead of structured RoB judgements.`);
+        }
+    }
+    phaseTimings.risk_of_bias = Date.now() - tRob;
+    // ── Phase 4: cost_effectiveness_model ─────────────────────────────
+    const tCe = Date.now();
+    let ceResults = undefined;
+    let ceSummaryText = "";
+    if (!input.skip_ce_model) {
+        const ce = input.ce_inputs ?? {};
+        const ceRes = await safeRun(() => deps.costEffectivenessModel({
+            intervention: input.drug,
+            comparator: "standard of care",
+            indication: input.indication,
+            time_horizon: "lifetime",
+            perspective: input.perspective,
+            clinical_inputs: {
+                efficacy_delta: ce.efficacy_delta ?? 0.25,
+            },
+            cost_inputs: {
+                drug_cost_annual: ce.drug_cost_annual ?? 1000,
+                comparator_cost_annual: ce.comparator_cost_annual ?? 0,
+                ae_cost: ce.ae_cost ?? 0,
+                admin_cost: ce.admin_cost ?? 0,
+            },
+            utility_inputs: ce.qaly_on_treatment !== undefined ||
+                ce.qaly_comparator !== undefined
+                ? {
+                    qaly_on_treatment: ce.qaly_on_treatment,
+                    qaly_comparator: ce.qaly_comparator,
+                }
+                : undefined,
+            psa_iterations: 1000,
+            run_psa: true,
+            output_format: "json",
+        }));
+        if (ceRes.ok) {
+            const ceContent = ceRes.value.content;
+            if (typeof ceContent === "string") {
+                try {
+                    ceResults = JSON.parse(ceContent);
+                }
+                catch {
+                    ceResults = ceContent;
+                }
+            }
+            else {
+                ceResults = ceContent;
+            }
+            if (isRecord(ceResults) &&
+                isRecord(ceResults.base_case)) {
+                const bc = ceResults
+                    .base_case;
+                const icer = bc.icer;
+                if (typeof icer === "number") {
+                    ceSummaryText = `Deterministic ICER: ${input.perspective === "nhs" ? "£" : "$"}${Math.round(icer).toLocaleString()} per QALY.`;
+                }
+            }
+            audit = addAssumption(audit, `Phase 4 (cost_effectiveness_model) ran 1000-iteration PSA. ${ceSummaryText}`);
+        }
+        else {
+            audit = addWarning(audit, `Phase 4 (cost_effectiveness_model) failed: ${ceRes.error}. hta_dossier Economic Evidence Summary will be flagged as gap.`);
+        }
+    }
+    else {
+        audit = addAssumption(audit, `Phase 4 (cost_effectiveness_model) skipped (skip_ce_model=true).`);
+    }
+    phaseTimings.cost_effectiveness_model = Date.now() - tCe;
+    // ── Phase 5: hta_dossier ──────────────────────────────────────────
+    const tDossier = Date.now();
+    const dossierRes = await safeRun(() => deps.htaDossier({
+        hta_body: input.hta_body,
+        submission_type: input.submission_type,
+        drug_name: input.drug,
+        indication: input.indication,
+        evidence_summary: screenedRecords.length > 0 ? screenedRecords : undefined,
+        rob_results: robResults,
+        model_results: ceResults,
+    }));
+    let dossierContent = "";
+    if (dossierRes.ok) {
+        dossierContent = asText(dossierRes.value);
+        audit = addAssumption(audit, `Phase 5 (hta_dossier) produced ${input.hta_body.toUpperCase()} ${input.submission_type.toUpperCase()} draft with ${screenedRecords.length} cited studies.`);
+    }
+    else {
+        audit = addWarning(audit, `Phase 5 (hta_dossier) failed: ${dossierRes.error}.`);
+    }
+    phaseTimings.hta_dossier = Date.now() - tDossier;
+    // ── Phase 6: validate_links ──────────────────────────────────────
+    // Scan the dossier output + screened records for URLs, validate up to 50.
+    const tValidate = Date.now();
+    const urlsFromDossier = extractUrls(dossierContent);
+    const urlsFromRecords = screenedRecords.map((r) => r.url).filter(Boolean);
+    const allUrls = Array.from(new Set([...urlsFromRecords, ...urlsFromDossier])).slice(0, 50);
+    let validationContent = "";
+    let validationCounts = { working: 0, browser_only: 0, broken: 0 };
+    if (allUrls.length > 0) {
+        const valRes = await safeRun(() => deps.validateLinks({ urls: allUrls }));
+        if (valRes.ok) {
+            validationContent = asText(valRes.value);
+            // Best-effort summary extraction
+            const valObj = valRes.value.content;
+            const valData = typeof valObj === "string"
+                ? (() => {
+                    try {
+                        return JSON.parse(valObj);
+                    }
+                    catch {
+                        return null;
+                    }
+                })()
+                : valObj;
+            if (isRecord(valData) &&
+                isRecord(valData.summary)) {
+                const s = valData.summary;
+                validationCounts = {
+                    working: Number(s.working ?? 0),
+                    browser_only: Number(s.browser_only ?? 0),
+                    broken: Number(s.broken ?? 0),
+                };
+            }
+            audit = addAssumption(audit, `Phase 6 (validate_links) checked ${allUrls.length} URLs: ${validationCounts.working} working, ${validationCounts.browser_only} browser-only, ${validationCounts.broken} broken.`);
+        }
+        else {
+            audit = addWarning(audit, `Phase 6 (validate_links) failed: ${valRes.error}.`);
+        }
+    }
+    phaseTimings.validate_links = Date.now() - tValidate;
+    const totalMs = Date.now() - t0;
+    audit = addAssumption(audit, `Total pipeline time: ${totalMs}ms.`);
+    // ── Render combined report ───────────────────────────────────────
+    const lines = [];
+    lines.push(`# HTA Submission Workflow — ${input.drug} (${input.indication})`);
+    lines.push("");
+    lines.push(`**Pipeline:** literature_search → screen_abstracts → risk_of_bias → cost_effectiveness_model → hta_dossier → validate_links`);
+    lines.push(`**Target:** ${input.hta_body.toUpperCase()} ${input.submission_type.toUpperCase()} · perspective: ${input.perspective}`);
+    lines.push(`**Total time:** ${totalMs}ms · 6 phases`);
+    lines.push("");
+    lines.push(`## Pipeline summary`);
+    lines.push("| Phase | Tool | Time (ms) | Outcome |");
+    lines.push("|-------|------|----------:|---------|");
+    lines.push(`| 1 | literature_search | ${phaseTimings.literature_search ?? 0} | ${literatureRecords.length} records via ${input.sources.join(", ")} |`);
+    lines.push(`| 2 | screen_abstracts | ${phaseTimings.screen_abstracts ?? 0} | ${screenedRecords.length} included |`);
+    lines.push(`| 3 | risk_of_bias | ${phaseTimings.risk_of_bias ?? 0} | ${robSummaryText || (robResults ? "assessed" : "skipped")} |`);
+    if (input.skip_ce_model) {
+        lines.push(`| 4 | cost_effectiveness_model | — | skipped |`);
+    }
+    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(`| 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.
+    lines.push(`## ${input.hta_body.toUpperCase()} dossier draft`);
+    lines.push("");
+    lines.push(dossierContent || "_(dossier phase failed — see warnings below)_");
+    lines.push("");
+    if (validationContent) {
+        lines.push(`## URL validation report`);
+        lines.push("");
+        lines.push(validationContent);
+        lines.push("");
+    }
+    lines.push(`## Audit`);
+    lines.push("");
+    lines.push(auditToMarkdown(audit));
+    return {
+        content: lines.join("\n"),
+        audit,
+        workflow_summary: {
+            total_ms: totalMs,
+            phase_timings_ms: phaseTimings,
+            n_records_searched: literatureRecords.length,
+            n_records_screened: screenedRecords.length,
+            n_urls_validated: allUrls.length,
+            url_validation_counts: validationCounts,
+        },
+    };
+}
+/**
+ * Production handler — wraps runHtaWorkflow with the real tool handlers
+ * imported lazily to avoid circular dependencies.
+ */
+export async function handleHtaWorkflow(rawInput) {
+    const [{ handleLiteratureSearch }, { handleScreenAbstracts }, { handleRiskOfBias }, { handleCostEffectivenessModel }, { handleHtaDossierPrep }, { handleValidateLinks },] = await Promise.all([
+        import("./literatureSearch.js"),
+        import("./screenAbstracts.js"),
+        import("./riskOfBias.js"),
+        import("./costEffectivenessModel.js"),
+        import("./htaDossierPrep.js"),
+        import("./validateLinks.js"),
+    ]);
+    return runHtaWorkflow(rawInput, {
+        literatureSearch: handleLiteratureSearch,
+        screenAbstracts: handleScreenAbstracts,
+        riskOfBias: handleRiskOfBias,
+        costEffectivenessModel: handleCostEffectivenessModel,
+        htaDossier: handleHtaDossierPrep,
+        validateLinks: handleValidateLinks,
+    });
+}
+export const htaWorkflowToolSchema = {
+    name: "hta.workflow",
+    description: "End-to-end HTA submission orchestrator. One call runs literature_search (with PRISMA-style stability via runs=N) → screen_abstracts (PICO filter) → risk_of_bias (auto RoB 2/ROBINS-I/AMSTAR-2) → cost_effectiveness_model (Markov + 1k PSA, defaults from indication) → hta_dossier (auto-GRADE downgrade from RoB output) → validate_links (post-hoc URL audit). Returns a combined report with per-phase timings, the full dossier draft, and the URL validation table. Use as a single-shot drop-in replacement for the 4-5 separate prompts a generic LLM would need to chain these tools manually. Each phase wrapped in safe-run so single-step failures do not abort the pipeline.",
+    annotations: {
+        title: "HTA Submission Workflow Orchestrator",
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+    inputSchema: {
+        type: "object",
+        properties: {
+            drug: { type: "string", description: "Drug or intervention name." },
+            indication: {
+                type: "string",
+                description: "Disease or condition (free text).",
+            },
+            hta_body: {
+                type: "string",
+                enum: HTA_BODIES,
+                default: "nice",
+                description: "Target HTA body for the dossier draft.",
+            },
+            submission_type: {
+                type: "string",
+                enum: SUBMISSION_TYPES,
+                default: "sta",
+            },
+            perspective: {
+                type: "string",
+                enum: PERSPECTIVES,
+                default: "nhs",
+                description: "Economic perspective for the cost-effectiveness model phase.",
+            },
+            drug_class: {
+                type: "string",
+                enum: DRUG_CLASSES,
+                default: "small_molecule",
+            },
+            is_orphan: {
+                type: "boolean",
+                default: false,
+                description: "Orphan-designated medicinal product. Affects JCA scope eligibility (orphans enter JCA scope 2028 vs 2030 for general medicinal products).",
+            },
+            pico: {
+                type: "object",
+                properties: {
+                    population: { type: "string" },
+                    intervention: { type: "string" },
+                    comparator: { type: "string" },
+                    outcomes: { type: "array", items: { type: "string" } },
+                },
+                description: "Optional PICO criteria for the screening phase (defaults derived from drug + indication).",
+            },
+            ce_inputs: {
+                type: "object",
+                description: "Optional cost-effectiveness model inputs. Sensible defaults applied when omitted (efficacy_delta=0.25; drug_cost_annual=1000; SoC=0).",
+                properties: {
+                    drug_cost_annual: { type: "number", minimum: 0 },
+                    comparator_cost_annual: { type: "number", minimum: 0 },
+                    efficacy_delta: { type: "number", minimum: 0, maximum: 1 },
+                    ae_cost: { type: "number", minimum: 0 },
+                    admin_cost: { type: "number", minimum: 0 },
+                    qaly_on_treatment: { type: "number", minimum: 0, maximum: 1 },
+                    qaly_comparator: { type: "number", minimum: 0, maximum: 1 },
+                },
+            },
+            sources: {
+                type: "array",
+                items: { type: "string", enum: SOURCES },
+                default: ["pubmed", "clinicaltrials"],
+            },
+            max_literature_results: {
+                type: "number",
+                minimum: 1,
+                maximum: 100,
+                default: 30,
+            },
+            literature_runs: {
+                type: "number",
+                minimum: 1,
+                maximum: 5,
+                default: 3,
+                description: "Number of dedup-stability passes for the literature_search phase. 3 is the project default for HTA-grade reproducibility.",
+            },
+            jurisdictions: {
+                type: "array",
+                items: {
+                    type: "string",
+                    enum: ["de", "fr", "it", "es", "nl", "uk", "eu_other"],
+                },
+                default: ["de", "fr", "it", "es", "nl"],
+            },
+            skip_ce_model: {
+                type: "boolean",
+                default: false,
+                description: "Skip the cost-effectiveness model phase (e.g., for clinical-only dossiers).",
+            },
+        },
+        required: ["drug", "indication"],
+    },
+};
+//# sourceMappingURL=htaWorkflow.js.map

package/dist/tools/htaWorkflow.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "heor-agent-mcp",
-  "version": "1.3.2",
+  "version": "1.4.0",
   "mcpName": "io.github.neptun2000/heor-agent",
   "license": "MIT",
   "author": "mnaumov",