@inflexa-ai/harness 0.16.0 → 0.17.0

package/dist/tools/lib/ncbi-utils.js

@@ -1,286 +1,2 @@
-/**
- * Shared NCBI E-utilities helpers for PubMed/PMC tools.
- *
- * Provides base URL constants, API key injection, and XML-to-article
- * mapping functions for PubMed and PMC DTD structures.
- */
-import { XMLParser } from "fast-xml-parser";
-// ── NCBI E-utilities base URLs ──────────────────────────────────────
-export const NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
-export const NCBI_IDCONV = "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0";
-// ── API key injection ───────────────────────────────────────────────
-/**
- * Append `api_key` and optional extra params to a base URL.
- * Omits the key when `apiKey` is undefined.
- */
-export function ncbiUrl(apiKey, base, params) {
-    const url = new URL(base);
-    if (apiKey) {
-        url.searchParams.set("api_key", apiKey);
-    }
-    for (const [k, v] of Object.entries(params)) {
-        if (v !== undefined) {
-            url.searchParams.set(k, String(v));
-        }
-    }
-    return url.toString();
-}
-// ── XML parser (shared, configured once) ────────────────────────────
-const xmlParser = new XMLParser({
-    ignoreAttributes: false,
-    attributeNamePrefix: "@_",
-    isArray: (name) => ["PubmedArticle", "Author", "MeshHeading", "AbstractText", "sec", "p", "record"].includes(name),
-    textNodeName: "#text",
-});
-function getItemValue(items, name) {
-    if (!items)
-        return "";
-    const arr = Array.isArray(items) ? items : [items];
-    const item = arr.find((i) => i["@_Name"] === name);
-    return item?.["#text"] ?? "";
-}
-function getAuthorsFromDocSum(items) {
-    if (!items)
-        return "";
-    const arr = Array.isArray(items) ? items : [items];
-    const authorList = arr.find((i) => i["@_Name"] === "AuthorList");
-    if (!authorList?.Item)
-        return "";
-    const authors = Array.isArray(authorList.Item) ? authorList.Item : [authorList.Item];
-    const names = authors.map((a) => a["#text"] ?? "").filter(Boolean);
-    if (names.length === 0)
-        return "";
-    if (names.length <= 3)
-        return names.join(", ");
-    return `${names[0]} et al.`;
-}
-/**
- * Parse esummary XML into PubMedSummary records.
- */
-export function parseEsummary(xml) {
-    const parsed = xmlParser.parse(xml);
-    const result = parsed?.eSummaryResult ?? parsed;
-    const docSums = result?.DocSum;
-    if (!docSums)
-        return [];
-    const docs = Array.isArray(docSums) ? docSums : [docSums];
-    return docs.map((doc) => {
-        const items = doc.Item;
-        const pubDate = getItemValue(items, "PubDate");
-        return {
-            pmid: String(doc.Id ?? ""),
-            title: getItemValue(items, "Title"),
-            journal: getItemValue(items, "FullJournalName") || getItemValue(items, "Source"),
-            year: pubDate ? String(pubDate).slice(0, 4) : "",
-            authors: getAuthorsFromDocSum(items),
-        };
-    });
-}
-/**
- * Parse efetch PubMed XML into ArticleDetail records.
- * `pmcId` is left null here — resolved separately via ID Converter.
- */
-export function parseEfetch(xml) {
-    const parsed = xmlParser.parse(xml);
-    const articleSet = parsed?.PubmedArticleSet;
-    if (!articleSet)
-        return [];
-    const articles = Array.isArray(articleSet.PubmedArticle) ? articleSet.PubmedArticle : articleSet.PubmedArticle ? [articleSet.PubmedArticle] : [];
-    return articles.map((entry) => {
-        const article = entry;
-        const medlineCitation = article.MedlineCitation;
-        const articleData = medlineCitation?.Article;
-        // PMID
-        const pmidObj = medlineCitation?.PMID;
-        const pmid = typeof pmidObj === "object" && pmidObj !== null ? String(pmidObj["#text"] ?? "") : String(pmidObj ?? "");
-        // Title
-        const title = String(articleData?.ArticleTitle ?? "");
-        // Abstract
-        const abstractObj = articleData?.Abstract;
-        let abstract = "";
-        if (abstractObj?.AbstractText) {
-            const texts = Array.isArray(abstractObj.AbstractText) ? abstractObj.AbstractText : [abstractObj.AbstractText];
-            abstract = texts
-                .map((t) => {
-                if (typeof t === "string")
-                    return t;
-                if (typeof t === "object" && t !== null) {
-                    const label = t["@_Label"];
-                    const text = t["#text"] ?? "";
-                    return label ? `${label}: ${text}` : String(text);
-                }
-                return String(t);
-            })
-                .join("\n\n");
-        }
-        // Authors
-        const authorListObj = articleData?.AuthorList;
-        const rawAuthors = authorListObj?.Author;
-        const authorArr = Array.isArray(rawAuthors) ? rawAuthors : rawAuthors ? [rawAuthors] : [];
-        const authors = authorArr.map((a) => {
-            if (a.CollectiveName)
-                return a.CollectiveName;
-            return [a.ForeName ?? a.Initials, a.LastName].filter(Boolean).join(" ");
-        });
-        // Journal + year
-        const journalObj = articleData?.Journal;
-        const journal = String(journalObj?.Title ?? journalObj?.ISOAbbreviation ?? "");
-        const journalIssue = journalObj?.JournalIssue;
-        const pubDate = journalIssue?.PubDate;
-        const year = String(pubDate?.Year ?? "");
-        // DOI
-        let doi = "";
-        const articleIdList = article.PubmedData?.ArticleIdList;
-        if (articleIdList?.ArticleId) {
-            const ids = Array.isArray(articleIdList.ArticleId) ? articleIdList.ArticleId : [articleIdList.ArticleId];
-            for (const idObj of ids) {
-                if (typeof idObj === "object" && idObj !== null) {
-                    const typed = idObj;
-                    if (typed["@_IdType"] === "doi") {
-                        doi = String(typed["#text"] ?? "");
-                    }
-                }
-            }
-        }
-        // MeSH terms
-        const meshList = medlineCitation?.MeshHeadingList;
-        const meshHeadings = meshList?.MeshHeading
-            ? Array.isArray(meshList.MeshHeading)
-                ? meshList.MeshHeading
-                : [meshList.MeshHeading]
-            : [];
-        const meshTerms = meshHeadings
-            .map((h) => {
-            const desc = h.DescriptorName;
-            if (typeof desc === "string")
-                return desc;
-            if (typeof desc === "object" && desc !== null)
-                return desc["#text"] ?? "";
-            return "";
-        })
-            .filter(Boolean);
-        return {
-            pmid,
-            title,
-            abstract,
-            authors,
-            journal,
-            year,
-            doi,
-            meshTerms,
-            pmcId: null, // resolved separately via ID Converter
-        };
-    });
-}
-// ── NCBI ID Converter mapping ───────────────────────────────────────
-/**
- * Parse ID Converter JSON response into a PMID → PMC ID map.
- * Returns only entries that have a PMC ID.
- */
-export function parseIdConvResponse(data) {
-    const map = new Map();
-    const typed = data;
-    if (!typed?.records)
-        return map;
-    for (const rec of typed.records) {
-        if (rec.pmid && rec.pmcid) {
-            map.set(rec.pmid, rec.pmcid);
-        }
-    }
-    return map;
-}
-/**
- * Parse PMC efetch XML into plain text with section structure.
- * Omits figures, tables, and supplementary material markup.
- */
-export function parsePmcFullText(xml) {
-    const parsed = xmlParser.parse(xml);
-    const articleSet = parsed?.["pmc-articleset"];
-    const article = articleSet?.article;
-    if (!article)
-        return null;
-    const body = article.body;
-    if (!body)
-        return null;
-    const sections = [];
-    const rawSecs = body.sec ? (Array.isArray(body.sec) ? body.sec : [body.sec]) : [];
-    for (const sec of rawSecs) {
-        extractSection(sec, sections);
-    }
-    // If no sections found, try to extract body text directly
-    if (sections.length === 0) {
-        const bodyText = extractParagraphs(body);
-        if (bodyText) {
-            sections.push({ heading: "", text: bodyText });
-        }
-    }
-    const fullText = sections.map((s) => (s.heading ? `## ${s.heading}\n\n${s.text}` : s.text)).join("\n\n");
-    return { fullText, sections };
-}
-function extractSection(sec, out) {
-    if (!sec || typeof sec !== "object")
-        return;
-    const s = sec;
-    const heading = typeof s.title === "string" ? s.title : "";
-    const text = extractParagraphs(s);
-    if (text) {
-        out.push({ heading, text });
-    }
-    // Recurse into nested sections
-    if (s.sec) {
-        const nested = Array.isArray(s.sec) ? s.sec : [s.sec];
-        for (const sub of nested) {
-            extractSection(sub, out);
-        }
-    }
-}
-function extractParagraphs(container) {
-    const paragraphs = container.p;
-    if (!paragraphs)
-        return "";
-    const pArr = Array.isArray(paragraphs) ? paragraphs : [paragraphs];
-    return pArr
-        .map((p) => {
-        if (typeof p === "string")
-            return p;
-        if (typeof p === "object" && p !== null) {
-            return flattenTextContent(p);
-        }
-        return String(p);
-    })
-        .filter(Boolean)
-        .join("\n\n");
-}
-/**
- * Recursively extract text content from a parsed XML node,
- * ignoring markup like <fig>, <table-wrap>, <xref>, etc.
- */
-function flattenTextContent(node) {
-    if (typeof node === "string")
-        return node;
-    if (typeof node === "number")
-        return String(node);
-    if (!node || typeof node !== "object")
-        return "";
-    const obj = node;
-    const parts = [];
-    for (const [key, value] of Object.entries(obj)) {
-        // Skip attributes and figure/table elements
-        if (key.startsWith("@_"))
-            continue;
-        if (key === "fig" || key === "table-wrap" || key === "supplementary-material")
-            continue;
-        if (key === "#text") {
-            parts.push(String(value));
-        }
-        else if (Array.isArray(value)) {
-            for (const item of value) {
-                parts.push(flattenTextContent(item));
-            }
-        }
-        else {
-            parts.push(flattenTextContent(value));
-        }
-    }
-    return parts.filter(Boolean).join("");
-}
+/** @deprecated Import NCBI authority contracts from literature/sources/pubmed. */
+export { NCBI_BASE, NCBI_IDCONV, ncbiUrl, parseEfetch, parseEsummary, parseIdConvResponse, parsePmcFullText } from "../../literature/sources/pubmed.js";

package/dist/tools/lib/pubmed-client.d.ts

@@ -4,18 +4,11 @@
  * Used by §3.11 (Key Papers), §3.10.4 (Preclinical literature), and the
  * pubmed-index Phase-1 collector.
  */
-import { type ArticleDetail, type ArticleSection, type PubMedSummary, type FullTextResult } from "./ncbi-utils.js";
+import { type ArticleDetail, type ArticleSection, type FullTextResult, type PubmedSearchOptions, type PubMedSummary } from "../../literature/sources/pubmed.js";
 export type { PubMedSummary, ArticleDetail, ArticleSection, FullTextResult };
-export interface SearchOptions {
-    maxResults?: number;
-    sort?: "relevance" | "date";
-    dateRange?: {
-        from: string;
-        to: string;
-    };
-}
+export type SearchOptions = PubmedSearchOptions;
 /** PubMed search via esearch + esummary. */
-export declare function searchPubmed(ncbiApiKey: string | undefined, query: string, options?: SearchOptions): Promise<{
+export declare function searchPubmed(ncbiApiKey: string | undefined, query: string, options?: SearchOptions, signal?: AbortSignal): Promise<{
     totalFound: number;
     results: PubMedSummary[];
 }>;
@@ -36,7 +29,7 @@ export interface BoundedArticleDetail extends ArticleDetail {
     meshTermCount: number;
 }
 /** Fetch full PubMed article details (efetch + ID Converter for PMC). */
-export declare function getArticleDetails(ncbiApiKey: string | undefined, pmids: string[]): Promise<{
+export declare function getArticleDetails(ncbiApiKey: string | undefined, pmids: string[], signal?: AbortSignal): Promise<{
     articles: ArticleDetail[];
     notFound: string[];
 }>;
@@ -76,6 +69,6 @@ export interface BoundedFullText {
  * Methods is worse than none) and admitted in document order until the budget
  * would be exceeded.
  */
-export declare function getArticleFullText(ncbiApiKey: string | undefined, pmcId: string, options?: FullTextOptions): Promise<BoundedFullText | null>;
+export declare function getArticleFullText(ncbiApiKey: string | undefined, pmcId: string, options?: FullTextOptions, signal?: AbortSignal): Promise<BoundedFullText | null>;
 /** Apply the section filter and character budget to a parsed full text. */
 export declare function boundFullText(parsed: FullTextResult, options?: FullTextOptions): BoundedFullText;

package/dist/tools/lib/pubmed-client.js

@@ -4,76 +4,27 @@
  * Used by §3.11 (Key Papers), §3.10.4 (Preclinical literature), and the
  * pubmed-index Phase-1 collector.
  */
-import { z } from "zod";
-import { apiFetch, apiFetchValidated, describeApiError } from "./api-utils.js";
-import { NCBI_BASE, NCBI_IDCONV, ncbiUrl, parseEsummary, parseEfetch, parseIdConvResponse, parsePmcFullText, } from "./ncbi-utils.js";
-// NCBI E-utilities JSON payloads, validated at the fetch boundary. Every field
-// is optional because the API omits absent values.
-const EsearchResponseSchema = z.object({
-    esearchresult: z.object({ idlist: z.array(z.string()).optional(), count: z.string().optional() }).optional(),
-});
-const IdConvResponseSchema = z.object({
-    records: z.array(z.object({ pmid: z.string().optional(), pmcid: z.string().optional() })).optional(),
-});
-/** PubMed search via esearch + esummary. */
-export async function searchPubmed(ncbiApiKey, query, options = {}) {
-    const maxResults = options.maxResults ?? 10;
-    const sort = options.sort ?? "relevance";
-    const esearchParams = {
-        db: "pubmed",
-        term: query,
-        retmax: maxResults,
-        retmode: "json",
-        sort: sort === "date" ? "pub+date" : "relevance",
-    };
-    if (options.dateRange) {
-        esearchParams.mindate = options.dateRange.from;
-        esearchParams.maxdate = options.dateRange.to;
-        esearchParams.datetype = "pdat";
-    }
-    const searchUrl = ncbiUrl(ncbiApiKey, `${NCBI_BASE}/esearch.fcgi`, esearchParams);
-    const searchResult = await apiFetchValidated(searchUrl, EsearchResponseSchema);
-    if (searchResult.isErr())
-        throw new Error(describeApiError(searchResult.error));
-    const idList = searchResult.value.esearchresult?.idlist ?? [];
-    const totalFound = parseInt(searchResult.value.esearchresult?.count ?? "0", 10);
-    if (idList.length === 0)
-        return { totalFound, results: [] };
-    const summaryUrl = ncbiUrl(ncbiApiKey, `${NCBI_BASE}/esummary.fcgi`, {
-        db: "pubmed",
-        id: idList.join(","),
-        retmode: "xml",
+import { createPubmedSource, } from "../../literature/sources/pubmed.js";
+function pubmedSource(ncbiApiKey) {
+    return createPubmedSource({
+        ...(ncbiApiKey === undefined ? {} : { apiKey: ncbiApiKey }),
+        maxRetries: 3,
+        retryDelayMs: 1_000,
+        timeoutMs: 90_000,
     });
-    const summaryResult = await apiFetch(summaryUrl, { parseAs: "text" });
-    if (summaryResult.isErr())
-        throw new Error(describeApiError(summaryResult.error));
-    return { totalFound, results: parseEsummary(summaryResult.value) };
+}
+function unwrap(result) {
+    if (result.status !== "ok")
+        throw new Error(result.detail);
+    return result.value;
+}
+/** PubMed search via esearch + esummary. */
+export async function searchPubmed(ncbiApiKey, query, options = {}, signal) {
+    return unwrap(await pubmedSource(ncbiApiKey).search(query, options, signal));
 }
 /** Fetch full PubMed article details (efetch + ID Converter for PMC). */
-export async function getArticleDetails(ncbiApiKey, pmids) {
-    const idString = pmids.join(",");
-    const efetchAsync = apiFetch(ncbiUrl(ncbiApiKey, `${NCBI_BASE}/efetch.fcgi`, {
-        db: "pubmed",
-        id: idString,
-        rettype: "xml",
-        retmode: "xml",
-    }), { parseAs: "text" });
-    const idConvAsync = apiFetchValidated(ncbiUrl(ncbiApiKey, NCBI_IDCONV, { ids: idString, format: "json" }), IdConvResponseSchema);
-    // Both requests run concurrently; each Result is awaited and handled below.
-    const efetchResult = await efetchAsync;
-    const idConvResult = await idConvAsync;
-    if (efetchResult.isErr())
-        throw new Error(describeApiError(efetchResult.error));
-    const articles = parseEfetch(efetchResult.value);
-    if (idConvResult.isOk()) {
-        const pmcMap = parseIdConvResponse(idConvResult.value);
-        for (const article of articles) {
-            article.pmcId = pmcMap.get(article.pmid) ?? null;
-        }
-    }
-    const foundPmids = new Set(articles.map((a) => a.pmid));
-    const notFound = pmids.filter((id) => !foundPmids.has(id));
-    return { articles, notFound };
+export async function getArticleDetails(ncbiApiKey, pmids, signal) {
+    return unwrap(await pubmedSource(ncbiApiKey).articleDetails(pmids, signal));
 }
 /** Trim the two unbounded list fields on each article, recording their true sizes. */
 export function boundArticleDetails(articles, options = {}) {
@@ -97,18 +48,8 @@ export function boundArticleDetails(articles, options = {}) {
  * Methods is worse than none) and admitted in document order until the budget
  * would be exceeded.
  */
-export async function getArticleFullText(ncbiApiKey, pmcId, options = {}) {
-    const numericId = pmcId.replace(/^PMC/i, "");
-    const url = ncbiUrl(ncbiApiKey, `${NCBI_BASE}/efetch.fcgi`, {
-        db: "pmc",
-        id: numericId,
-        rettype: "xml",
-        retmode: "xml",
-    });
-    const result = await apiFetch(url, { parseAs: "text" });
-    if (result.isErr())
-        throw new Error(describeApiError(result.error));
-    const parsed = parsePmcFullText(result.value);
+export async function getArticleFullText(ncbiApiKey, pmcId, options = {}, signal) {
+    const parsed = unwrap(await pubmedSource(ncbiApiKey).fetchFullText(pmcId, signal));
     if (!parsed)
         return null;
     return boundFullText(parsed, options);

package/dist/tools/research/generate-analogy-report.js

@@ -23,7 +23,7 @@ import { finalText, runAgent } from "../../loop/run-agent.js";
 import { passthroughStep } from "../../loop/run-step.js";
 import { defineTool } from "../define-tool.js";
 // Cross-domain search tools the analogical-reasoner uses.
-import { searchSemanticScholarTool } from "./search-semantic-scholar.js";
+import { createSearchSemanticScholarTool } from "./search-semantic-scholar.js";
 import { searchArxivTool } from "./search-arxiv.js";
 import { createSearchGithubReposTool } from "./search-github-repos.js";
 // Biology literature — reused for analogies that land back in biology.
@@ -156,7 +156,7 @@ function buildConversionPrompt(rawOutput) {
 export function createGenerateAnalogyReportTool(deps) {
     const ncbi = createNcbiTools(deps.bioKeys);
     const reasonerTools = [
-        searchSemanticScholarTool,
+        createSearchSemanticScholarTool({ ...(deps.bioKeys.semanticScholar === undefined ? {} : { apiKey: deps.bioKeys.semanticScholar }) }),
         searchArxivTool,
         createSearchGithubReposTool({ githubToken: deps.bioKeys.github }),
         ncbi.pubmed,

package/dist/tools/research/index.d.ts

@@ -14,3 +14,4 @@ export * from "./context7-docs.js";
 export * from "./search-semantic-scholar.js";
 export * from "./search-arxiv.js";
 export * from "./search-github-repos.js";
+export * from "./resolve-citation.js";

package/dist/tools/research/index.js

@@ -14,3 +14,4 @@ export * from "./context7-docs.js";
 export * from "./search-semantic-scholar.js";
 export * from "./search-arxiv.js";
 export * from "./search-github-repos.js";
+export * from "./resolve-citation.js";

package/dist/tools/research/inspect-run.d.ts

@@ -53,7 +53,7 @@ declare function formatRun(r: CortexRunRow, verbose: boolean, exposePaths?: bool
     synthesisReason?: string | undefined;
     runId: string;
     workflowName: string;
-    status: "running" | "completed" | "failed" | "partial" | "canceled" | "suspended_insufficient_funds";
+    status: "partial" | "running" | "completed" | "failed" | "canceled" | "suspended_insufficient_funds";
     startedAt: string;
     completedAt: string | null;
     planId: string | null;

package/dist/tools/research/literature-reviewer.d.ts

@@ -19,6 +19,7 @@ import { type Tool } from "../define-tool.js";
 import { type BioToolKeys } from "../bio/keys.js";
 import type { Logger } from "../../lib/logger.js";
 import type { UsageRecorder } from "../../billing/usage-recorder.js";
+import type { CitationResolver } from "../../citations/types.js";
 export interface LiteratureReviewerDeps {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
@@ -30,6 +31,8 @@ export interface LiteratureReviewerDeps {
     readonly bioKeys: BioToolKeys;
     /** LLM usage-accounting seam for the child loop; omitted falls back to the no-op recorder. */
     readonly usageRecorder?: UsageRecorder;
+    /** Shared bibliographic verification service; all agent surfaces share its pacing/cache. */
+    readonly citationResolver: CitationResolver;
 }
 /** Build the `literature_reviewer` delegation tool bound to its provider. */
 export declare function createLiteratureReviewerTool(deps: LiteratureReviewerDeps): Tool;

package/dist/tools/research/literature-reviewer.js

@@ -27,6 +27,7 @@ import { genePreclinicalProfileTool } from "../bio/gene-preclinical-profile.js";
 import { lookupAnnotationTool } from "../bio/lookup-annotation.js";
 import { searchGeneTool } from "../bio/search-gene.js";
 import { searchInteractionsTool } from "../bio/search-interactions.js";
+import { createResolveCitationTool } from "./resolve-citation.js";
 /** Sub-agent identity — appended to `callPath`, set as `agentId`. */
 const AGENT_ID = "literature-reviewer";
 /** Multi-tool research budget — search → read → synthesize over many genes. */
@@ -40,6 +41,7 @@ export function createLiteratureReviewerTool(deps) {
         lookupAnnotationTool,
         searchInteractionsTool,
         ncbi.pubmed,
+        createResolveCitationTool(deps.citationResolver),
         chemDb.drugGeneInteractions,
         genePreclinicalProfileTool,
     ];

package/dist/tools/research/resolve-citation.d.ts

@@ -0,0 +1,3 @@
+import { type CitationResolver } from "../../citations/types.js";
+import { type Tool } from "../define-tool.js";
+export declare function createResolveCitationTool(resolver: CitationResolver): Tool;

package/dist/tools/research/resolve-citation.js

@@ -0,0 +1,15 @@
+import { ok } from "neverthrow";
+import { CitationInputSchema } from "../../citations/types.js";
+import { defineTool } from "../define-tool.js";
+export function createResolveCitationTool(resolver) {
+    return defineTool({
+        id: "resolve_citation",
+        description: "Verify one supplied citation against applicable bibliographic authorities. " +
+            "Use this for 'does this reference exist and does its metadata agree?', not for topical literature discovery. " +
+            "Returns source-labelled records, field comparisons, conflicts, coverage, and one of verified, metadata_mismatch, " +
+            "not_found, unverifiable, or inconclusive. Source failure never becomes not_found.",
+        inputSchema: CitationInputSchema,
+        describeCall: ({ citation }) => `verify ${citation}`,
+        execute: async (input, ctx) => ok(await resolver.resolveOne(input, { signal: ctx.signal })),
+    });
+}

package/dist/tools/research/search-arxiv.d.ts

@@ -1,10 +1,6 @@
-/**
- * Search arXiv for preprints. Returns Atom XML which we parse without a
- * dependency. arXiv is the primary source for ML / physics / math /
- * control-theory preprints; Semantic Scholar lags it by months.
- *
- * Same wire call and envelope as the legacy tool. Stateless HTTP; no deps.
- */
+/** Search arXiv for preprints through the shared authority client. */
+import { type ArxivPaper } from "../../literature/sources/arxiv.js";
+export { parseArxivAtom, type ArxivPaper } from "../../literature/sources/arxiv.js";
 type SearchArxivOutput = {
     success: false;
     error: string;
@@ -13,20 +9,8 @@ type SearchArxivOutput = {
     success: true;
     papers: ArxivPaper[];
 };
-export interface ArxivPaper {
-    id: string;
-    title: string;
-    abstract: string;
-    authors: string[];
-    published: string;
-    categories: string[];
-    url: string;
-    pdfUrl?: string;
-}
-export declare function parseArxivAtom(xml: string): ArxivPaper[];
 export declare const searchArxivTool: import("../define-tool.js").Tool<{
     query: string;
     limit: number;
     categories?: string[] | undefined;
 }, SearchArxivOutput>;
-export {};