@mantra-ai/core 0.1.0

package/dist/sources/medrxiv/client.js.map

@@ -0,0 +1 @@
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package/dist/sources/medrxiv/shared.d.ts

@@ -0,0 +1,7 @@
+export declare const MEDRXIV_ACCEPT_XML = "application/xml,text/xml;q=0.9,*/*;q=0.8";
+export declare const MEDRXIV_HTML_ACCEPT = "text/html,application/xhtml+xml";
+export declare const MEDRXIV_ACCEPT_LANGUAGE = "en-GB,en;q=0.9";
+export declare const MEDRXIV_BROWSER_UA = "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36";
+export declare function looksLikeJatsXml(source: string | null | undefined): boolean;
+export declare const safePreview: (value: string, limit?: number) => string;
+//# sourceMappingURL=shared.d.ts.map

package/dist/sources/medrxiv/shared.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"shared.d.ts","sourceRoot":"","sources":["../../../src/sources/medrxiv/shared.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,kBAAkB,6CAA6C,CAAC;AAC7E,eAAO,MAAM,mBAAmB,oCAAoC,CAAC;AACrE,eAAO,MAAM,uBAAuB,mBAAmB,CAAC;AACxD,eAAO,MAAM,kBAAkB,0HAC0F,CAAC;AAE1H,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,GAAG,OAAO,CAO3E;AAED,eAAO,MAAM,WAAW,GAAI,OAAO,MAAM,EAAE,cAAW,KAAG,MACb,CAAC"}

package/dist/sources/medrxiv/shared.js

@@ -0,0 +1,18 @@
+export const MEDRXIV_ACCEPT_XML = "application/xml,text/xml;q=0.9,*/*;q=0.8";
+export const MEDRXIV_HTML_ACCEPT = "text/html,application/xhtml+xml";
+export const MEDRXIV_ACCEPT_LANGUAGE = "en-GB,en;q=0.9";
+export const MEDRXIV_BROWSER_UA = "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36";
+export function looksLikeJatsXml(source) {
+    if (!source)
+        return false;
+    const slice = source.slice(0, 16384).toLowerCase();
+    if (!slice.includes("<article"))
+        return false;
+    if (slice.includes("xmlns:jats") || slice.includes("xmlns:xlink"))
+        return true;
+    if (slice.includes("<front") || slice.includes("<article-meta"))
+        return true;
+    return /<body[\s>]/.test(slice) || /<article-body[\s>]/.test(slice);
+}
+export const safePreview = (value, limit = 400) => value.slice(0, limit).replace(/\s+/g, " ");
+//# sourceMappingURL=shared.js.map

package/dist/sources/medrxiv/shared.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"shared.js","sourceRoot":"","sources":["../../../src/sources/medrxiv/shared.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,kBAAkB,GAAG,0CAA0C,CAAC;AAC7E,MAAM,CAAC,MAAM,mBAAmB,GAAG,iCAAiC,CAAC;AACrE,MAAM,CAAC,MAAM,uBAAuB,GAAG,gBAAgB,CAAC;AACxD,MAAM,CAAC,MAAM,kBAAkB,GAC7B,uHAAuH,CAAC;AAE1H,MAAM,UAAU,gBAAgB,CAAC,MAAiC;IAChE,IAAI,CAAC,MAAM;QAAE,OAAO,KAAK,CAAC;IAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,WAAW,EAAE,CAAC;IACnD,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,UAAU,CAAC;QAAE,OAAO,KAAK,CAAC;IAC9C,IAAI,KAAK,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC;QAAE,OAAO,IAAI,CAAC;IAC/E,IAAI,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,KAAK,CAAC,QAAQ,CAAC,eAAe,CAAC;QAAE,OAAO,IAAI,CAAC;IAC7E,OAAO,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,oBAAoB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AACtE,CAAC;AAED,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,KAAa,EAAE,KAAK,GAAG,GAAG,EAAU,EAAE,CAChE,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC"}

package/dist/sources/plos/client.d.ts

@@ -0,0 +1,13 @@
+export declare function fetchPlosJatsXml(doi: string): Promise<string>;
+export interface PlosSearchDoc {
+    id?: string;
+    title_display?: string;
+    journal?: string;
+    article_type?: string;
+    author_display?: string[];
+    abstract?: string[] | string;
+    body?: string[] | string;
+    copyright?: string[] | string;
+}
+export declare function fetchPlosSearchDocByDoi(doi: string): Promise<PlosSearchDoc | null>;
+//# sourceMappingURL=client.d.ts.map

package/dist/sources/plos/client.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"client.d.ts","sourceRoot":"","sources":["../../../src/sources/plos/client.ts"],"names":[],"mappings":"AA4EA,wBAAsB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAiEnE;AAED,MAAM,WAAW,aAAa;IAC5B,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,CAAC,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC;IACzB,SAAS,CAAC,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC;CAE/B;AAED,wBAAsB,uBAAuB,CAC3C,GAAG,EAAE,MAAM,GACV,OAAO,CAAC,aAAa,GAAG,IAAI,CAAC,CAgB/B"}

package/dist/sources/plos/client.js

@@ -0,0 +1,147 @@
+const UA = process.env.UA || "drylab-reveng-api/1.0";
+function journalSlugFromDoi(doi) {
+    // DOI pattern: 10.1371/journal.pone.XXXX
+    const suffix = doi.split("/")[1] || "";
+    const map = {
+        "journal.pone": "plosone",
+        "journal.pbio": "plosbiology",
+        "journal.pcbi": "ploscompbiol",
+        "journal.pgen": "plosgenetics",
+        "journal.ppat": "plospathogens",
+        "journal.pmed": "plosmedicine",
+        "journal.pntd": "plosntds",
+        "journal.pgph": "plosglobalpubhealth",
+        // Add additional known mappings as needed
+    };
+    const key = Object.keys(map).find((k) => suffix.startsWith(k));
+    return key ? map[key] : "plosone";
+}
+function buildPlosXmlUrlCandidates(doi) {
+    const primarySlug = journalSlugFromDoi(doi);
+    const slugCandidates = [primarySlug];
+    // Historical/alternate slugs that might appear
+    if (primarySlug === "plosbiology")
+        slugCandidates.push("plosbiol");
+    if (primarySlug === "plosglobalpubhealth")
+        slugCandidates.push("plosglobalpublichealth");
+    const suffix = doi.split("/")[1] || ""; // e.g., journal.pbio.3003277
+    const idCandidates = [doi, suffix, `info:doi/${doi}`, `info:doi/${suffix}`];
+    const typeCandidates = ["xml", "XML"];
+    const downloadFlag = [undefined, "1"];
+    const urls = [];
+    for (const slug of slugCandidates) {
+        const base = `https://journals.plos.org/${slug}/article/file`;
+        for (const id of idCandidates) {
+            for (const t of typeCandidates) {
+                for (const dl of downloadFlag) {
+                    const params = new URLSearchParams();
+                    params.set("id", id);
+                    params.set("type", t);
+                    if (dl)
+                        params.set("download", dl);
+                    urls.push(`${base}?${params.toString()}`);
+                }
+            }
+        }
+    }
+    return urls;
+}
+async function fetchWithRetry(url, init = {}, retries = 2) {
+    const timeoutMs = init.timeoutMs ?? 15000;
+    const controller = new AbortController();
+    const id = setTimeout(() => controller.abort(), timeoutMs);
+    try {
+        const res = await fetch(url, { ...init, signal: controller.signal });
+        if (!res.ok) {
+            if (retries > 0 && res.status >= 500) {
+                await new Promise((r) => setTimeout(r, 300 * (3 - retries)));
+                return fetchWithRetry(url, init, retries - 1);
+            }
+            throw new Error(`PLOS fetch failed: ${res.status} ${res.statusText}`);
+        }
+        return res;
+    }
+    finally {
+        clearTimeout(id);
+    }
+}
+export async function fetchPlosJatsXml(doi) {
+    const urls = buildPlosXmlUrlCandidates(doi);
+    const headers = {
+        Accept: "application/xml, text/xml;q=0.9, */*;q=0.8",
+        "User-Agent": UA || "drylab-reveng-api/1.0",
+    };
+    let lastError = undefined;
+    for (const url of urls) {
+        try {
+            const res = await fetchWithRetry(url, { timeoutMs: 20000, headers });
+            const text = await res.text();
+            if (text && text.includes("<article"))
+                return text;
+            lastError = new Error("PLOS returned non-JATS content");
+        }
+        catch (e) {
+            // Continue trying other URL shapes on 404/400, store error
+            lastError = e;
+            continue;
+        }
+    }
+    // As a final fallback, try to discover the XML link from the article landing page
+    const baseSlug = journalSlugFromDoi(doi);
+    const landingCandidates = [
+        `https://journals.plos.org/${baseSlug}/article?id=${encodeURIComponent(doi)}`,
+        `https://journals.plos.org/${baseSlug}/article?id=${encodeURIComponent(`info:doi/${doi}`)}`,
+        `https://journals.plos.org/${baseSlug}/article?id=${doi}`,
+    ];
+    const htmlHeaders = {
+        Accept: "text/html, */*;q=0.8",
+        "User-Agent": headers["User-Agent"],
+    };
+    for (const lurl of landingCandidates) {
+        try {
+            const res = await fetchWithRetry(lurl, {
+                timeoutMs: 20000,
+                headers: htmlHeaders,
+            });
+            const html = await res.text();
+            // Support single-quoted, double-quoted, and &amp; encoded query strings
+            const m = /href=["']([^"']*\/article\/file[^"']*(?:type=xml|type=XML)[^"']*)["']/i.exec(html);
+            if (m && m[1]) {
+                const href = m[1].replace(/&amp;/g, "&");
+                const absolute = href.startsWith("http")
+                    ? href
+                    : new URL(href, lurl).toString();
+                const r2 = await fetchWithRetry(absolute, {
+                    timeoutMs: 20000,
+                    headers,
+                });
+                const text = await r2.text();
+                if (text && text.includes("<article"))
+                    return text;
+            }
+        }
+        catch (e) {
+            lastError = e;
+        }
+    }
+    throw lastError instanceof Error
+        ? lastError
+        : new Error("PLOS fetch failed for all URL candidates");
+}
+export async function fetchPlosSearchDocByDoi(doi) {
+    // API: http://api.plos.org/search?q=id:"DOI"&rows=1&wt=json
+    const base = "http://api.plos.org/search";
+    const q = `id:"${doi}"`;
+    const url = `${base}?q=${encodeURIComponent(q)}&rows=1&wt=json`;
+    const headers = {
+        Accept: "application/json",
+        "User-Agent": UA || "drylab-reveng-api/1.0",
+    };
+    const res = await fetchWithRetry(url, { timeoutMs: 15000, headers });
+    const data = (await res.json());
+    const doc = data && data.response && Array.isArray(data.response.docs)
+        ? data.response.docs[0]
+        : null;
+    return doc;
+}
+//# sourceMappingURL=client.js.map

package/dist/sources/plos/client.js.map

@@ -0,0 +1 @@
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package/dist/sources/preprint-discovery.d.ts

@@ -0,0 +1,55 @@
+/**
+ * Shared preprint record discovery utilities for bioRxiv and medRxiv.
+ *
+ * Both servers expose the same API structure via api.biorxiv.org/details,
+ * return the same collection shape, and use the same version/date selection
+ * logic. This module parameterizes those operations by server name and domain.
+ */
+export type PreprintServer = "biorxiv" | "medrxiv";
+export type PreprintRecord = {
+    url: string;
+    version?: number | null;
+    date?: string;
+};
+/**
+ * Normalize an input id/DOI to the "core" numeric id by stripping
+ * the 10.1101/ prefix, any URL prefix, and version suffixes.
+ */
+export declare function normPreprintCore(idOrDoi: string, server: PreprintServer): string;
+/**
+ * Build the bioRxiv/medRxiv details API URL for a given core id.
+ */
+export declare function preprintDetailsApiUrl(idOrDoi: string, server: PreprintServer): string;
+/**
+ * Convert a relative JATS XML path to an absolute URL for the given server.
+ */
+export declare function toAbsolutePreprintUrl(u: string | null | undefined, server: PreprintServer): string | null;
+/**
+ * Fetch the details JSON for a preprint from the API.
+ */
+export declare function fetchPreprintDetailsJson(idOrDoi: string, server: PreprintServer, UA?: string, debug?: boolean): Promise<any | null>;
+/**
+ * Parse a version number from any value, returning null if invalid.
+ */
+export declare function parseVersionNumber(v: any): number | null;
+/**
+ * Normalize the `collection` array from the details API response
+ * into typed PreprintRecord objects with absolute JATS XML URLs.
+ */
+export declare function normalizeCollectionItems(apiJson: any, server: PreprintServer): PreprintRecord[];
+/**
+ * Pick the best record from a list of preprint records, preferring
+ * an exact version match if requested, otherwise the latest by
+ * version number then date.
+ */
+export declare function pickBestRecord(records: PreprintRecord[], preferVersion?: number | null): PreprintRecord | null;
+/**
+ * High-level: discover the best JATS XML record for a preprint via the API.
+ * Returns the record with an absolute URL, or null if not found.
+ */
+export declare function discoverPreprintRecord(idOrDoi: string, server: PreprintServer, opts?: {
+    UA?: string;
+    preferVersion?: number | null;
+    debug?: boolean;
+}): Promise<PreprintRecord | null>;
+//# sourceMappingURL=preprint-discovery.d.ts.map

package/dist/sources/preprint-discovery.d.ts.map

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package/dist/sources/preprint-discovery.js

@@ -0,0 +1,115 @@
+/**
+ * Normalize an input id/DOI to the "core" numeric id by stripping
+ * the 10.1101/ prefix, any URL prefix, and version suffixes.
+ */
+export function normPreprintCore(idOrDoi, server) {
+    const domain = server === "biorxiv" ? "biorxiv.org" : "medrxiv.org";
+    return String(idOrDoi)
+        .trim()
+        .replace(new RegExp(`^https?://(www\\.)?${domain.replace(".", "\\.")}/content/10\\.1101/`, "i"), "")
+        .replace(/^10\.1101\//i, "")
+        .replace(/v\d+$/i, "");
+}
+/**
+ * Build the bioRxiv/medRxiv details API URL for a given core id.
+ */
+export function preprintDetailsApiUrl(idOrDoi, server) {
+    const core = normPreprintCore(idOrDoi, server);
+    return `https://api.biorxiv.org/details/${server}/10.1101/${core}/na/json`;
+}
+/**
+ * Convert a relative JATS XML path to an absolute URL for the given server.
+ */
+export function toAbsolutePreprintUrl(u, server) {
+    if (!u)
+        return null;
+    if (/^https?:\/\//i.test(u))
+        return u;
+    const domain = server === "biorxiv" ? "www.biorxiv.org" : "www.medrxiv.org";
+    return `https://${domain}${u.startsWith("/") ? "" : "/"}${u}`;
+}
+/**
+ * Fetch the details JSON for a preprint from the API.
+ */
+export async function fetchPreprintDetailsJson(idOrDoi, server, UA = "drylab-reveng-api/1.0", debug = false) {
+    const url = preprintDetailsApiUrl(idOrDoi, server);
+    debug && console.log(`[${server}] details url:`, url);
+    const res = await fetch(url, {
+        headers: { Accept: "application/json", "User-Agent": UA },
+    });
+    if (!res.ok) {
+        debug && console.log(`[${server}] details status:`, res.status);
+        return null;
+    }
+    const json = await res.json();
+    debug &&
+        console.log(`[${server}] details ok, items:`, Array.isArray(json?.collection)
+            ? json.collection.length
+            : 0);
+    return json;
+}
+/**
+ * Parse a version number from any value, returning null if invalid.
+ */
+export function parseVersionNumber(v) {
+    const n = parseInt(String(v ?? ""), 10);
+    return Number.isFinite(n) ? n : null;
+}
+/**
+ * Normalize the `collection` array from the details API response
+ * into typed PreprintRecord objects with absolute JATS XML URLs.
+ */
+export function normalizeCollectionItems(apiJson, server) {
+    const items = Array.isArray(apiJson?.collection)
+        ? apiJson.collection
+        : [];
+    const getJats = (it) => it?.jatsxml || it?.jats_xml_path || it?.jats_xml || null;
+    return items
+        .map((item) => {
+        const url = toAbsolutePreprintUrl(getJats(item), server);
+        if (!url)
+            return null;
+        const version = parseVersionNumber(item?.version);
+        const date = typeof item?.date === "string" ? item.date : undefined;
+        return { url, version, date };
+    })
+        .filter((x) => Boolean(x?.url));
+}
+/**
+ * Pick the best record from a list of preprint records, preferring
+ * an exact version match if requested, otherwise the latest by
+ * version number then date.
+ */
+export function pickBestRecord(records, preferVersion) {
+    if (!records.length)
+        return null;
+    const sorted = records.slice().sort((a, b) => {
+        const versionDiff = (b.version ?? -Infinity) - (a.version ?? -Infinity);
+        if (versionDiff !== 0)
+            return versionDiff;
+        const dateA = a.date ? Date.parse(a.date) || 0 : 0;
+        const dateB = b.date ? Date.parse(b.date) || 0 : 0;
+        return dateB - dateA;
+    });
+    if (preferVersion && Number.isFinite(preferVersion)) {
+        const exact = sorted.find((r) => r.version === preferVersion);
+        if (exact)
+            return exact;
+    }
+    return sorted[0] ?? null;
+}
+/**
+ * High-level: discover the best JATS XML record for a preprint via the API.
+ * Returns the record with an absolute URL, or null if not found.
+ */
+export async function discoverPreprintRecord(idOrDoi, server, opts) {
+    const debug = opts?.debug ?? false;
+    const json = await fetchPreprintDetailsJson(idOrDoi, server, opts?.UA, debug);
+    if (!json)
+        return null;
+    const records = normalizeCollectionItems(json, server);
+    const record = pickBestRecord(records, opts?.preferVersion);
+    debug && console.log(`[${server}] extracted jats record:`, record?.url);
+    return record ?? null;
+}
+//# sourceMappingURL=preprint-discovery.js.map

package/dist/sources/preprint-discovery.js.map

@@ -0,0 +1 @@
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package/dist/types/expand.d.ts

@@ -0,0 +1,5 @@
+import { z } from "zod";
+export declare const WorkExpandableFields: z.ZodEnum<["all", "sections", "blocks", "assets", "citations"]>;
+export declare function processExpandParameter(expand?: string[] | string): Set<string>;
+export type WorkExpandableField = z.infer<typeof WorkExpandableFields>;
+//# sourceMappingURL=expand.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"expand.d.ts","sourceRoot":"","sources":["../../src/types/expand.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAGxB,eAAO,MAAM,oBAAoB,iEAE2B,CAAC;AAG7D,wBAAgB,sBAAsB,CACpC,MAAM,CAAC,EAAE,MAAM,EAAE,GAAG,MAAM,GACzB,GAAG,CAAC,MAAM,CAAC,CAcb;AAGD,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC"}

package/dist/types/expand.js

@@ -0,0 +1,20 @@
+import { z } from "zod";
+// Shared expandable fields enum for all work endpoints
+export const WorkExpandableFields = z
+    .enum(["all", "sections", "blocks", "assets", "citations"])
+    .describe("Fields that can be expanded in work responses");
+// Helper function to process expand parameter
+export function processExpandParameter(expand) {
+    // Handle both string and array inputs
+    const expandArray = Array.isArray(expand) ? expand : expand ? [expand] : [];
+    const expandSet = new Set(expandArray);
+    // Handle 'all' expansion - expand everything
+    if (expandSet.has("all")) {
+        expandSet.add("sections");
+        expandSet.add("blocks");
+        expandSet.add("assets");
+        expandSet.add("citations");
+    }
+    return expandSet;
+}
+//# sourceMappingURL=expand.js.map

package/dist/types/expand.js.map

@@ -0,0 +1 @@
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package/dist/types/methods-types.d.ts

@@ -0,0 +1,37 @@
+export type MethodComponent = {
+    id: string;
+    doi: string;
+    order: number;
+    title: string;
+    raw_text: string;
+    mentioned_figures?: string[];
+    mentioned_tables?: string[];
+    mentioned_supplementary_files?: string[];
+    cited_references?: CitedReference[] | null;
+    software_tools?: SoftwareTool[] | null;
+    error?: string | null;
+};
+export type Methods = {
+    doi: string;
+    url: string;
+    pmcid: string | null;
+    methods_section: MethodComponent[] | null;
+    error?: string | null;
+};
+export interface SoftwareTool {
+    name_in_paper: string;
+    version_in_paper?: string;
+    language_hint?: string;
+    operating_system_context?: string[];
+    access_point_raw?: string;
+    role_in_paper?: string;
+    is_web_platform_or_service?: boolean;
+    package_ecosystem_hint?: string;
+}
+export interface CitedReference {
+    id: string;
+    doi?: string;
+    text_reference?: string;
+    full_citation?: string;
+}
+//# sourceMappingURL=methods-types.d.ts.map

package/dist/types/methods-types.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/methods-types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=methods-types.js.map

package/dist/types/methods-types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"methods-types.js","sourceRoot":"","sources":["../../src/types/methods-types.ts"],"names":[],"mappings":""}

package/dist/types/multi-input-types.d.ts

@@ -0,0 +1,57 @@
+export interface MultipartFile {
+    type: "file";
+    fieldname: string;
+    filename: string;
+    encoding: string;
+    mimetype: string;
+    file: NodeJS.ReadableStream;
+    toBuffer(): Promise<Buffer>;
+}
+export interface InputResult {
+    providedDoi: string | null;
+    uploadedFile?: MultipartFile;
+    pdfSource: Buffer | string | null;
+    sourceFileName: string | null;
+    pdfReachable: boolean;
+    inputType: "file" | "doi" | null;
+}
+export interface ToolInfo {
+    conda_package?: string;
+    channel?: string;
+    language_hint?: "C" | "C++" | "Java" | "Perl" | "Python" | "R" | string;
+    notes?: string;
+    r_package_name?: string;
+    r_source?: "Bioconductor" | "CRAN" | string;
+    aliases?: string[];
+    website?: string;
+    publication_doi?: string;
+}
+export interface ToolMap {
+    [canonicalKey: string]: ToolInfo;
+}
+export interface ProcessedToolEntry {
+    originalName: string;
+    originalVersion?: string;
+    condaPackage?: string;
+    condaVersionSpecifier?: string;
+    channel?: string;
+    matchType: "exact_alias" | "exact_light" | "exact_aggressive" | "similar" | "none" | "not_conda_installable";
+    notes: string[];
+    toolInfo?: ToolInfo;
+}
+export interface NormalizedTool {
+    name_in_paper: string;
+    version_in_paper?: string;
+    _toolInfo: {
+        conda_package?: string;
+        channel?: string;
+        language_hint?: "C" | "C++" | "Java" | "Perl" | "Python" | "R" | string;
+        notes?: string;
+        r_package_name?: string;
+        r_source?: "Bioconductor" | "CRAN" | string;
+        aliases?: string[];
+        website?: string;
+        publication_doi?: string;
+    };
+}
+//# sourceMappingURL=multi-input-types.d.ts.map

package/dist/types/multi-input-types.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/multi-input-types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=multi-input-types.js.map

package/dist/types/multi-input-types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"multi-input-types.js","sourceRoot":"","sources":["../../src/types/multi-input-types.ts"],"names":[],"mappings":""}