@mantra-ai/core 0.1.0

package/dist/works/id/resolveIds/assign.js.map

@@ -0,0 +1 @@
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package/dist/works/id/resolveIds/flags.d.ts

@@ -0,0 +1,11 @@
+import type { CompleteIds } from "../../types";
+export declare function computeIsPreprint(applied: CompleteIds, isPreprintDoi: (d?: string | null) => boolean): boolean;
+export declare function computeIsOpenAccess({ oaBest, oaAny, isPreprint, license, crossrefLic, }: {
+    oaBest: any;
+    oaAny: boolean;
+    isPreprint: boolean;
+    license?: string;
+    crossrefLic?: string;
+}): boolean;
+export declare function synthesizeBestPdfUrl(applied: CompleteIds): string | undefined;
+//# sourceMappingURL=flags.d.ts.map

package/dist/works/id/resolveIds/flags.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"flags.d.ts","sourceRoot":"","sources":["../../../../src/works/id/resolveIds/flags.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAM/C,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,WAAW,EACpB,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,MAAM,GAAG,IAAI,KAAK,OAAO,WAQ9C;AAED,wBAAgB,mBAAmB,CAAC,EAClC,MAAM,EACN,KAAK,EACL,UAAU,EACV,OAAO,EACP,WAAW,GACZ,EAAE;IACD,MAAM,EAAE,GAAG,CAAC;IACZ,KAAK,EAAE,OAAO,CAAC;IACf,UAAU,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB,WAQA;AAED,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,GAAG,SAAS,CAS7E"}

package/dist/works/id/resolveIds/flags.js

@@ -0,0 +1,27 @@
+const looksCreativeCommons = (lic) => !!lic &&
+    /(creativecommons|cc-?by|cc0|cc-?by-?sa|cc-?by-?nc|cc-?by-?nd)/i.test(lic);
+export function computeIsPreprint(applied, isPreprintDoi) {
+    return Boolean(applied.biorxivId ||
+        applied.medrxivId ||
+        applied.arxivId ||
+        isPreprintDoi(applied.doi));
+}
+export function computeIsOpenAccess({ oaBest, oaAny, isPreprint, license, crossrefLic, }) {
+    return (oaBest?.is_oa === true ||
+        oaAny ||
+        isPreprint ||
+        looksCreativeCommons(license || crossrefLic) ||
+        false);
+}
+export function synthesizeBestPdfUrl(applied) {
+    if (applied.arxivId)
+        return `https://arxiv.org/pdf/${applied.arxivId}.pdf`;
+    if (applied.pmcid)
+        return `https://www.ncbi.nlm.nih.gov/pmc/articles/${applied.pmcid}/pdf`;
+    if (applied.biorxivId && /v\d+$/i.test(applied.biorxivId))
+        return `https://www.biorxiv.org/content/10.1101/${applied.biorxivId}.full.pdf`;
+    if (applied.medrxivId && /v\d+$/i.test(applied.medrxivId))
+        return `https://www.medrxiv.org/content/10.1101/${applied.medrxivId}.full.pdf`;
+    return undefined;
+}
+//# sourceMappingURL=flags.js.map

package/dist/works/id/resolveIds/flags.js.map

@@ -0,0 +1 @@
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package/dist/works/id/resolveIds/idctx.d.ts

@@ -0,0 +1,4 @@
+export declare function normalizeVersionLabel(value?: string | null): string | null;
+export declare function stripVersionSuffix(value?: string | null): string | null;
+export declare function hasVersionSuffix(value?: string | null): boolean;
+//# sourceMappingURL=idctx.d.ts.map

package/dist/works/id/resolveIds/idctx.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"idctx.d.ts","sourceRoot":"","sources":["../../../../src/works/id/resolveIds/idctx.ts"],"names":[],"mappings":"AAAA,wBAAgB,qBAAqB,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,MAAM,GAAG,IAAI,CAY1E;AAED,wBAAgB,kBAAkB,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,MAAM,GAAG,IAAI,CAGvE;AAED,wBAAgB,gBAAgB,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,OAAO,CAG/D"}

package/dist/works/id/resolveIds/idctx.js

@@ -0,0 +1,25 @@
+export function normalizeVersionLabel(value) {
+    if (!value)
+        return null;
+    const v = String(value).trim().toLowerCase();
+    if (v === "published")
+        return "published";
+    const m = v.match(/^v\s*(\d+)$/i);
+    if (m) {
+        const n = Number(m[1]);
+        if (Number.isFinite(n) && n >= 1)
+            return `v${n}`;
+    }
+    return null;
+}
+export function stripVersionSuffix(value) {
+    if (!value)
+        return null;
+    return String(value).replace(/v\d+$/i, "");
+}
+export function hasVersionSuffix(value) {
+    if (!value)
+        return false;
+    return /v\d+$/i.test(String(value));
+}
+//# sourceMappingURL=idctx.js.map

package/dist/works/id/resolveIds/idctx.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"idctx.js","sourceRoot":"","sources":["../../../../src/works/id/resolveIds/idctx.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,qBAAqB,CAAC,KAAqB;IACzD,IAAI,CAAC,KAAK;QAAE,OAAO,IAAI,CAAC;IACxB,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAE7C,IAAI,CAAC,KAAK,WAAW;QAAE,OAAO,WAAW,CAAC;IAE1C,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;IAClC,IAAI,CAAC,EAAE,CAAC;QACN,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACvB,IAAI,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC,EAAE,CAAC;IACnD,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,KAAqB;IACtD,IAAI,CAAC,KAAK;QAAE,OAAO,IAAI,CAAC;IACxB,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;AAC7C,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,KAAqB;IACpD,IAAI,CAAC,KAAK;QAAE,OAAO,KAAK,CAAC;IACzB,OAAO,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;AACtC,CAAC"}

package/dist/works/id/resolveIds/index.d.ts

@@ -0,0 +1,13 @@
+import type { ActionsExternalType, CompleteIds } from "../../types";
+import { type LoggerLike } from "../../util/debug";
+/** ---- Orchestrator ---- */
+export declare function resolveIds(externalIdType: ActionsExternalType, rawId: string, opts?: {
+    logger?: LoggerLike | {
+        log?: LoggerLike;
+    };
+    debug?: boolean;
+    cid?: string;
+}): Promise<{
+    completeIds: CompleteIds;
+}>;
+//# sourceMappingURL=index.d.ts.map

package/dist/works/id/resolveIds/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/works/id/resolveIds/index.ts"],"names":[],"mappings":"AAiBA,OAAO,KAAK,EACV,mBAAmB,EAEnB,WAAW,EAEZ,MAAM,aAAa,CAAC;AAGrB,OAAO,EAAkB,KAAK,UAAU,EAAE,MAAM,kBAAkB,CAAC;AA+LnE,6BAA6B;AAC7B,wBAAsB,UAAU,CAC9B,cAAc,EAAE,mBAAmB,EACnC,KAAK,EAAE,MAAM,EACb,IAAI,CAAC,EAAE;IACL,MAAM,CAAC,EAAE,UAAU,GAAG;QAAE,GAAG,CAAC,EAAE,UAAU,CAAA;KAAE,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd,GACA,OAAO,CAAC;IAAE,WAAW,EAAE,WAAW,CAAA;CAAE,CAAC,CA+avC"}

package/dist/works/id/resolveIds/index.js

@@ -0,0 +1,498 @@
+import { normalizeExternalId, } from "../normalize-external-id";
+import { normalizeAndMaybeResolveToDOI, normalizeDOI, normalizePMID, normalizePMCID, normalizeArXivId, } from "../normalize-ids";
+import { resolveArxivToDoi, resolvePmcidToDoi, resolvePmidToDoi, shouldQueryCrossrefForDoi, } from "../resolve";
+import { inferSourceKind } from "../../util/source";
+import { parseDebugFlag } from "../../util/debug";
+import { normalizeIds } from "../../util/normalize";
+import { parseArxivIdFromUrl, parseArxivIdFromDoi, parseBiorxivMedrxivIdFromDoi, } from "../../util/parse";
+import { fetchOpenAlexWorkByKey, fetchOpenAlexWorkByDoi, } from "../../adapters/openalex";
+import { resolveDoiToPmidPmcidViaEpmc } from "../../adapters/europepmc";
+import { enrichFromCrossref } from "../../adapters/crossref";
+import { inferVersionLabel } from "./versioning";
+import { computeIsPreprint, computeIsOpenAccess, synthesizeBestPdfUrl, } from "./flags";
+/** ---- small local helpers (behavioral no-ops, reduce duplication) ---- */
+function stripHtmlLike(input) {
+    if (!input || typeof input !== "string")
+        return undefined;
+    const s = input
+        .replace(/<[^>]+>/g, " ") // drop tags
+        .replace(/\s+/g, " ")
+        .trim();
+    return s || undefined;
+}
+function reconstructOpenAlexAbstract(inv) {
+    if (!inv || typeof inv !== "object")
+        return undefined;
+    // Rebuild by positions
+    const positions = [];
+    for (const [token, idxs] of Object.entries(inv)) {
+        for (const i of idxs)
+            positions.push({ pos: i, token });
+    }
+    positions.sort((a, b) => a.pos - b.pos);
+    const text = positions.map((p) => p.token).join(" ");
+    return text && text.trim() ? text : undefined;
+}
+function ensureLandingUrlFromDoi(r) {
+    if (r.doi && !r.landingUrl)
+        r.landingUrl = `https://doi.org/${r.doi}`;
+}
+function pickCrossrefLicenseUrl(crossref) {
+    return Array.isArray(crossref?.license)
+        ? crossref.license[0]?.URL || crossref.license[0]?.["content-version"]
+        : undefined;
+}
+function parseCrossrefFirstDate(cr) {
+    if (!cr)
+        return undefined;
+    const picks = [
+        cr["published-online"],
+        cr["published-print"],
+        cr["created"],
+    ].filter(Boolean);
+    for (const d of picks) {
+        // Crossref date-parts format: { "date-parts": [[YYYY, M?, D?]] }
+        const parts = Array.isArray(d?.["date-parts"]) && Array.isArray(d["date-parts"][0])
+            ? d["date-parts"][0]
+            : null;
+        if (!parts || !parts.length)
+            continue;
+        const [Y, M = 1, D = 1] = parts;
+        if (Y)
+            return new Date(Date.UTC(Y, M - 1, D)).toISOString();
+    }
+    return undefined;
+}
+function parseOpenAlexDate(oa) {
+    const y = oa?.publication_year;
+    const dt = oa?.publication_date; // e.g., "2024-05-12"
+    if (dt && /^\d{4}-\d{2}-\d{2}$/.test(dt)) {
+        return new Date(dt + "T00:00:00Z").toISOString();
+    }
+    if (y && Number.isInteger(y)) {
+        return new Date(Date.UTC(y, 0, 1)).toISOString();
+    }
+    return undefined;
+}
+function pickBestLicense({ crossref, openalex, existing, }) {
+    // Crossref
+    const crLicArr = Array.isArray(crossref?.license) ? crossref.license : [];
+    const crLic = crLicArr.length
+        ? crLicArr[0].URL || crLicArr[0]["content-version"]
+        : undefined;
+    // OpenAlex
+    const oaLic = openalex?.best_oa_location?.license || undefined;
+    return ((crLic && String(crLic)) ||
+        (oaLic && String(oaLic)) ||
+        (existing && String(existing)) ||
+        undefined);
+}
+/** Prefer a DOI lookup, otherwise fall back to the provided external key. */
+async function fetchOpenAlexPreferDoiThenKey(doi, externalIdType, normalizedInput, rawId) {
+    if (doi) {
+        const byDoi = await fetchOpenAlexWorkByDoi(doi);
+        if (byDoi.ok)
+            return byDoi;
+    }
+    return fetchOpenAlexWorkByKey(externalIdType, normalizedInput ?? rawId);
+}
+/** Consolidated arXiv inference across all signals (existing → Crossref → OpenAlex → arXiv DOI) */
+function inferArxivId({ existing, crossref, openalex, doi, logger, }) {
+    // 1) existing (already normalized upstream)
+    if (existing)
+        return existing;
+    // 2) Crossref relation: look for arXiv
+    try {
+        const rel = crossref?.relation ?? {};
+        const relVals = Object.values(rel).flat();
+        for (const r of relVals) {
+            const id = r?.id;
+            const arx = id?.startsWith("arXiv:")
+                ? id.replace(/^arXiv:/i, "")
+                : parseArxivIdFromUrl(id ?? "");
+            if (arx)
+                return normalizeArXivId(arx)?.replace(/v\d+$/i, "");
+        }
+    }
+    catch (err) {
+        logger?.warn?.({ err, source: "crossref", step: "extractArxivId" }, "resolveIds.extractArxivId: failed parsing Crossref relations");
+    }
+    // 3) OpenAlex: locations/source
+    if (openalex) {
+        const primary = openalex.primary_location || null;
+        const best = openalex.best_oa_location || null;
+        const allLocs = [primary, best, ...(openalex.locations || [])].filter(Boolean);
+        for (const loc of allLocs) {
+            const url = loc?.landing_page_url || loc?.pdf_url || undefined;
+            const arx = parseArxivIdFromUrl(url || undefined);
+            if (arx)
+                return normalizeArXivId(arx)?.replace(/v\d+$/i, "");
+            const src = loc?.source?.display_name || loc?.source?.id || "";
+            if (/arxiv/i.test(src)) {
+                const arx2 = parseArxivIdFromUrl(url || undefined);
+                if (arx2)
+                    return normalizeArXivId(arx2)?.replace(/v\d+$/i, "");
+            }
+        }
+    }
+    // 4) DOI minted by DataCite for arXiv
+    if (doi) {
+        const fromDoi = parseArxivIdFromDoi(doi);
+        if (fromDoi)
+            return normalizeArXivId(fromDoi)?.replace(/v\d+$/i, "");
+    }
+    return undefined;
+}
+/** ---- Orchestrator ---- */
+export async function resolveIds(externalIdType, rawId, opts) {
+    const cid = opts?.cid;
+    const rawLogger = opts?.logger;
+    const logger = rawLogger && typeof rawLogger === "object" && "log" in rawLogger
+        ? rawLogger.log
+        : rawLogger;
+    const shouldDebug = parseDebugFlag(opts?.debug) || parseDebugFlag(process.env.DEBUG_ADD_IDS);
+    const debug = (obj, msg) => {
+        if (!shouldDebug)
+            return;
+        try {
+            const payload = { tag: "resolveIds", ...obj };
+            logger?.warn?.({ correlationId: cid, ...payload }, msg);
+        }
+        catch { }
+    };
+    // 1) Normalize the provided identifier
+    const normalizedInput = normalizeExternalId(externalIdType, rawId) ?? undefined;
+    // capture original rxiv cores for version suffix restoration
+    const originalBiorxivId = externalIdType === "biorxivId"
+        ? String(normalizedInput ?? rawId)
+            .trim()
+            .replace(/^10\.1101\//i, "")
+        : null;
+    const originalMedrxivId = externalIdType === "medrxivId"
+        ? String(normalizedInput ?? rawId)
+            .trim()
+            .replace(/^10\.1101\//i, "")
+        : null;
+    debug({ externalIdType, rawId, normalizedInput }, "ids.start");
+    const result = {};
+    const confirmedBy = new Set();
+    const upstreamErrors = [];
+    const assignCanon = (ids) => Object.assign(result, normalizeIds({
+        ...result,
+        ...Object.fromEntries(Object.entries(ids).filter(([, v]) => v !== undefined && v !== null)),
+    }));
+    // Preserve arXiv / medrxiv up front (so we never lose them during DOI resolution)
+    if (externalIdType === "arxivId" && (normalizedInput ?? rawId)) {
+        const canon = normalizeArXivId(normalizedInput ?? rawId);
+        if (canon)
+            assignCanon({ arxivId: canon.replace(/v\d+$/i, "") });
+    }
+    if (externalIdType === "medrxivId" && (normalizedInput ?? rawId)) {
+        const core = String(normalizedInput ?? rawId)
+            .trim()
+            .replace(/^10\.1101\//i, "");
+        if (core)
+            assignCanon({ medrxivId: core });
+    }
+    if (externalIdType === "biorxivId" && (normalizedInput ?? rawId)) {
+        const core = String(normalizedInput ?? rawId)
+            .trim()
+            .replace(/^10\.1101\//i, "");
+        if (core)
+            assignCanon({ biorxivId: core });
+    }
+    debug({ partial: { ...result } }, "ids.after_preserve");
+    // 2) Resolve to DOI (single place)
+    let doi = null;
+    if (externalIdType !== "openalexId") {
+        const map = {
+            doi: "doi",
+            pmid: "pmid",
+            pmcid: "pmcid",
+            arxivId: "arxiv",
+            biorxivId: "biorxiv",
+            medrxivId: "medrxiv",
+            openalexId: "openalex",
+        };
+        const mapped = map[externalIdType];
+        if (mapped && mapped !== "openalex") {
+            const res = await normalizeAndMaybeResolveToDOI(mapped, normalizedInput ?? rawId, {
+                resolvePmidToDoi,
+                resolvePmcidToDoi,
+                resolveArxivToDoi,
+            });
+            if (res.ok && res.data.type === "doi") {
+                doi = res.data.value;
+                debug({ doi }, "ids.doi_resolved.initial");
+            }
+            else if (res.ok) {
+                const t = res.data.type;
+                if (t === "pmid")
+                    assignCanon({ pmid: res.data.value });
+                if (t === "pmcid")
+                    assignCanon({ pmcid: res.data.value });
+                if (t === "arxiv")
+                    assignCanon({ arxivId: res.data.value });
+                if (t === "biorxiv")
+                    assignCanon({ biorxivId: res.data.value });
+                if (t === "medrxiv")
+                    assignCanon({ medrxivId: res.data.value });
+                debug({ type: t, value: res.data.value, partial: { ...result } }, "ids.no_doi_fallback");
+            }
+        }
+    }
+    // 3) Crossref enrichment (single spot)
+    let crossref = null;
+    if (doi && shouldQueryCrossrefForDoi(doi)) {
+        const cr = await enrichFromCrossref(doi);
+        crossref = cr.crossref;
+        doi = cr.doi; // possibly refined DOI casing from Crossref
+        if (crossref) {
+            confirmedBy.add("crossref");
+            const { license, landingUrl, publisher, journal, year } = cr.enriched;
+            // NEW: extract Crossref title safely (array or string)
+            const crTitleRaw = crossref?.title;
+            const crTitle = Array.isArray(crTitleRaw)
+                ? crTitleRaw[0] ?? null
+                : typeof crTitleRaw === "string"
+                    ? crTitleRaw
+                    : null;
+            assignCanon({
+                doi: doi ?? undefined,
+                license,
+                landingUrl,
+                publisher,
+                journal,
+                year,
+                // NEW: carry a human-readable title
+                title: crTitle && crTitle.trim() ? crTitle : undefined,
+            });
+            debug({ doi, license, landingUrl, publisher, journal, year, title: crTitle }, "ids.crossref.enriched");
+        }
+        else if (cr.adapterError) {
+            upstreamErrors.push({
+                source: "crossref",
+                status: cr.adapterError.status,
+                reason: cr.adapterError.reason,
+            });
+            assignCanon({ doi: doi || undefined });
+            debug({ doi, adapterError: cr.adapterError }, "ids.crossref.error");
+        }
+        else {
+            assignCanon({ doi: doi || undefined });
+            debug({ doi }, "ids.crossref.miss");
+        }
+    }
+    else if (doi) {
+        assignCanon({ doi });
+        debug({ doi }, "ids.crossref.skipped");
+    }
+    // Consolidated landing URL synthesis (single place after DOI phase)
+    ensureLandingUrlFromDoi(result);
+    // 4) OpenAlex enrichment (wrapped)
+    const oaResult = await fetchOpenAlexPreferDoiThenKey(doi, externalIdType, normalizedInput, rawId);
+    const openalex = oaResult.ok ? oaResult.data : null;
+    if (!oaResult.ok && oaResult.reason !== "not_found") {
+        upstreamErrors.push({
+            source: "openalex",
+            status: oaResult.status,
+            reason: oaResult.reason,
+        });
+    }
+    if (openalex) {
+        confirmedBy.add("openalex");
+        const ids = openalex.ids || {};
+        const oaId = (ids.openalex || openalex.id || "").replace(/^https?:\/\/(www\.)?openalex\.org\//i, "");
+        const oaDoi = ids.doi ? normalizeDOI(ids.doi) : null;
+        const oaPmid = ids.pmid ? normalizePMID(ids.pmid) : null;
+        const oaPmcid = ids.pmcid ? normalizePMCID(ids.pmcid) : null;
+        const oaTitle = openalex.title || openalex.display_name || null;
+        if (!result.title &&
+            oaTitle &&
+            typeof oaTitle === "string" &&
+            oaTitle.trim()) {
+            assignCanon({ title: oaTitle });
+        }
+        // Merge core identifiers (DOI first, but allow OpenAlex to backfill if missing)
+        assignCanon({
+            doi: result.doi || oaDoi || undefined,
+            pmid: result.pmid || oaPmid || undefined,
+            pmcid: result.pmcid || oaPmcid || undefined,
+            openalexId: result.openalexId || oaId || undefined,
+            // license/landingUrl/journal/publisher/year only if still missing
+            landingUrl: result.landingUrl ||
+                openalex.best_oa_location?.landing_page_url ||
+                openalex.primary_location?.landing_page_url ||
+                undefined,
+            license: result.license ||
+                openalex.best_oa_location?.license ||
+                undefined,
+            journal: result.journal ||
+                openalex.host_venue?.display_name ||
+                openalex.primary_location?.source?.display_name ||
+                openalex.best_oa_location?.source?.display_name ||
+                undefined,
+            publisher: result.publisher || openalex.host_venue?.publisher || undefined,
+            year: typeof result.year === "number"
+                ? result.year
+                : openalex.publication_year || undefined,
+        });
+        // Derive biorxiv/medrxiv from DOI & venue (only if still missing)
+        const venueName = openalex.host_venue?.display_name || null;
+        const rxiv = parseBiorxivMedrxivIdFromDoi(result.doi || oaDoi || null, venueName);
+        if (rxiv)
+            assignCanon(rxiv);
+    }
+    // arXiv inference (single pass from all signals)
+    {
+        const arxiv = inferArxivId({
+            existing: result.arxivId ?? null,
+            crossref,
+            openalex,
+            doi: result.doi ?? null,
+            logger,
+        });
+        if (arxiv)
+            assignCanon({ arxivId: arxiv });
+    }
+    // 5) EuropePMC backfill for pmid/pmcid (if missing and DOI present)
+    if (result.doi && (!result.pmid || !result.pmcid)) {
+        const epResult = await resolveDoiToPmidPmcidViaEpmc(result.doi);
+        if (epResult.adapterError) {
+            upstreamErrors.push({
+                source: "europepmc",
+                status: epResult.adapterError.status,
+                reason: epResult.adapterError.reason,
+            });
+        }
+        if (epResult.result) {
+            confirmedBy.add("europepmc");
+            assignCanon({
+                pmid: result.pmid || epResult.result.pmid,
+                pmcid: result.pmcid || epResult.result.pmcid,
+            });
+            debug({ ep: epResult.result }, "ids.epmc.backfill");
+        }
+    }
+    // --- ABSTRACT (Crossref → OpenAlex) ---
+    let abstractBest;
+    const crAbsRaw = crossref && typeof crossref === "object" ? crossref.abstract ?? null : null;
+    const crAbs = stripHtmlLike(typeof crAbsRaw === "string" ? crAbsRaw : undefined);
+    if (crAbs) {
+        abstractBest = crAbs;
+    }
+    else if (openalex) {
+        abstractBest = reconstructOpenAlexAbstract(openalex.abstract_inverted_index);
+    }
+    if (abstractBest)
+        result.abstract = abstractBest;
+    // --- BEST LICENSE (Crossref → OpenAlex → existing) ---
+    const bestLicense = pickBestLicense({
+        crossref,
+        openalex,
+        existing: result.license ?? null,
+    });
+    if (bestLicense)
+        result.bestLicense = bestLicense;
+    // --- FIRST PUBLISHED DATE (Crossref → OpenAlex) ---
+    const firstPublishedAt = parseCrossrefFirstDate(crossref) ||
+        parseOpenAlexDate(openalex) ||
+        undefined;
+    if (firstPublishedAt)
+        result.firstPublishedAt = firstPublishedAt;
+    // 6) Last resort: arXiv → DOI, then synthesize landing URL once
+    if (!result.doi && result.arxivId) {
+        const d = await resolveArxivToDoi(result.arxivId);
+        if (d)
+            assignCanon({ doi: d });
+        if (result.doi)
+            ensureLandingUrlFromDoi(result);
+        debug({ doi: result.doi }, "ids.arxiv.final_doi_backfill");
+    }
+    // ---- Final normalization & flags ----
+    const final = normalizeIds(result);
+    // restore version suffixes if user provided explicit vN cores originally
+    const normalizeVersionSuffix = (value) => value.replace(/v(\d+)$/i, (_, d) => `v${d}`);
+    if (originalBiorxivId &&
+        /v\d+$/i.test(originalBiorxivId) &&
+        (!final.biorxivId || !/v\d+$/i.test(final.biorxivId))) {
+        final.biorxivId = normalizeVersionSuffix(originalBiorxivId);
+    }
+    if (originalMedrxivId &&
+        /v\d+$/i.test(originalMedrxivId) &&
+        (!final.medrxivId || !/v\d+$/i.test(final.medrxivId))) {
+        final.medrxivId = normalizeVersionSuffix(originalMedrxivId);
+    }
+    debug({ final }, "ids.final.before_apply");
+    // normalizeIds already applied all canonical normalization; no second pass needed
+    const applied = final;
+    // ---- Version inference (new, robust) ----
+    const crossrefType = crossref?.type ?? null;
+    const crossrefSubtype = crossref?.subtype ?? null;
+    const openalexVenueName = openalex?.host_venue?.display_name ?? null;
+    const openalexIsPreprintVenue = Boolean(/arxiv|bio?rxiv|medrxiv|osf|preprint/i.test(openalexVenueName || ""));
+    const versionInf = await inferVersionLabel({
+        doi: applied.doi ?? null,
+        arxivId: applied.arxivId ?? null,
+        biorxivId: applied.biorxivId ?? null,
+        medrxivId: applied.medrxivId ?? null,
+        landingUrl: applied.landingUrl ?? null,
+        journal: applied.journal ?? null,
+        openalexHostVenue: openalexVenueName,
+    }, {
+        crossrefType,
+        crossrefSubtype,
+        openalexVenueName,
+        openalexIsPreprintVenue,
+    });
+    applied.version = versionInf.label; // "published" or "vN"
+    applied.versionStage = versionInf.stage; // "journal" | "preprint" | "unknown"
+    applied.versionConfidence = versionInf.confidence;
+    applied.versionEvidence = versionInf.evidence;
+    const sourceKind = inferSourceKind({
+        biorxivId: applied.biorxivId ?? null,
+        medrxivId: applied.medrxivId ?? null,
+        arxivId: applied.arxivId ?? null,
+        pmcid: applied.pmcid ?? null,
+        landingUrl: applied.landingUrl ?? null,
+        openalexHostVenue: openalexVenueName,
+    });
+    applied.sourceKind = sourceKind;
+    applied.sourceName = openalexVenueName ?? applied.publisher ?? null;
+    // ---- Flags (single place) ----
+    const crossrefLic = pickCrossrefLicenseUrl(crossref);
+    // keep existing isPreprint logic, but you can also short-circuit using versionStage if desired
+    const isPreprintDoi = (d) => !!d &&
+        /^(10\.1101\/|10\.48550\/(?:arxiv\.|arxiv:)|10\.31219\/osf\.io\/|10\.31234\/osf\.io\/|10\.7287\/peerj\.preprints)/i.test(d);
+    const isPreprint = computeIsPreprint(applied, isPreprintDoi);
+    applied.isPreprint = isPreprint;
+    const oaBest = openalex?.best_oa_location;
+    const oaAny = (openalex?.locations || []).some((l) => l?.is_oa === true);
+    const isOpenAccess = computeIsOpenAccess({
+        oaBest,
+        oaAny,
+        isPreprint,
+        license: applied.license,
+        crossrefLic,
+    });
+    applied.isOpenAccess = !!isOpenAccess;
+    // bestPdfUrl (single place)
+    let bestPdfUrl = oaBest?.pdf_url ??
+        (openalex?.locations || []).find((l) => l?.pdf_url)?.pdf_url ??
+        synthesizeBestPdfUrl(applied) ??
+        undefined;
+    if (bestPdfUrl)
+        applied.bestPdfUrl = bestPdfUrl;
+    applied.abstract = result.abstract || undefined;
+    applied.isOpenAccess = !!applied.isOpenAccess;
+    applied.bestLicense =
+        result.bestLicense || applied.license || undefined;
+    applied.firstPublishedAt =
+        result.firstPublishedAt || undefined;
+    applied.confirmedBy = [...confirmedBy];
+    if (upstreamErrors.length > 0) {
+        applied.upstreamErrors = upstreamErrors;
+    }
+    return { completeIds: applied };
+}
+//# sourceMappingURL=index.js.map

package/dist/works/id/resolveIds/index.js.map

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