@mantra-ai/core 0.1.0

package/dist/normalization/jats/utils/references.d.ts

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+export type CollectedReference = {
+    id?: string;
+    label?: string;
+    raw?: string;
+    text?: string;
+    xml?: string;
+    xml_minimal?: string;
+    articleTitle?: string;
+    sourceTitle?: string;
+    year?: number;
+    volume?: string;
+    issue?: string;
+    fpage?: string;
+    lpage?: string;
+    doi?: string;
+    pmid?: string;
+    pmcid?: string;
+    authors?: Array<{
+        surname?: string;
+        givenNames?: string;
+    }>;
+    pubType?: string;
+};
+export declare function collectReferences(back: any, domPO?: any): CollectedReference[];
+export declare function cleanupReferenceText(s: string): string;
+//# sourceMappingURL=references.d.ts.map

package/dist/normalization/jats/utils/references.d.ts.map

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package/dist/normalization/jats/utils/references.js

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+import { poText } from "./po/text";
+import { normalizeArray } from "./strings";
+import { asString } from "./strings";
+import { escapeXml } from "./strings";
+import { getText } from "./xml";
+import { poFindFirstByLocal } from "./po/query";
+import { poFindFirstByLocalAttr } from "./po/query";
+import { poChildren } from "./po/nodes";
+import { poSerialize } from "./po/serialize";
+import { poSerializeCitationMinimal } from "./po/serialize";
+function cleanupCitationText(s) {
+    if (!s)
+        return s;
+    let out = s;
+    // Collapse multiple whitespace
+    out = out.replace(/\s+/g, " ");
+    // No space before punctuation like , . ; : ) ] } ! ?
+    out = out.replace(/\s+([,;:.!?\)\]\}])/g, "$1");
+    // No space after opening punctuation like ( [ {
+    out = out.replace(/([\(\[\{])\s+/g, "$1");
+    // Ensure space after comma/period if followed by word/number
+    out = out.replace(/([,.])(\S)/g, "$1 $2");
+    // Fix spaced en-dash in page ranges
+    out = out.replace(/\s*[–-]\s*/g, "–");
+    // Trim
+    out = out.trim();
+    // Remove duplicate terminal punctuation
+    out = out.replace(/([.!?]){2,}$/g, "$1");
+    return out;
+}
+function serializeCitationMinimalFromObject(obj) {
+    const authors = [];
+    for (const nm of normalizeArray(obj?.["string-name"]).concat(normalizeArray(obj?.name))) {
+        const s = formatNameNode(nm);
+        if (s) {
+            const [surname, given] = s.split(/\s+(.+)?/).filter(Boolean);
+            const gn = given ? `<given-names>${escapeXml(given)}</given-names>` : "";
+            authors.push(`<string-name><surname>${escapeXml(surname || "")}</surname>${gn}</string-name>`);
+        }
+    }
+    const etal = asString(obj?.etal)
+        ? `<etal>${escapeXml(asString(obj?.etal))}</etal>`
+        : "";
+    const title = asString(obj?.["article-title"]) || asString(obj?.title) || undefined;
+    const source = asString(obj?.source) || undefined;
+    const volume = asString(obj?.volume) || undefined;
+    const issue = asString(obj?.issue) || undefined;
+    const fpage = asString(obj?.fpage) || undefined;
+    const lpage = asString(obj?.lpage) || undefined;
+    const year = asString(obj?.year) || undefined;
+    const parts = [];
+    if (authors.length)
+        parts.push(authors.join(""));
+    if (etal)
+        parts.push(etal);
+    if (title)
+        parts.push(`<article-title>${escapeXml(title)}</article-title>`);
+    if (source)
+        parts.push(`<source>${escapeXml(source)}</source>`);
+    if (volume)
+        parts.push(`<volume>${escapeXml(volume)}</volume>`);
+    if (issue)
+        parts.push(`<issue>${escapeXml(issue)}</issue>`);
+    if (fpage)
+        parts.push(`<fpage>${escapeXml(fpage)}</fpage>`);
+    if (lpage)
+        parts.push(`<lpage>${escapeXml(lpage)}</lpage>`);
+    if (year)
+        parts.push(`<year>${escapeXml(year)}</year>`);
+    if (!parts.length)
+        return undefined;
+    return `<citation>${parts.join("")}</citation>`;
+}
+// Parse a JATS citation node into structured fields + formatted string.
+function parseCitationNode(node) {
+    if (!node)
+        return undefined;
+    const authorNames = extractAuthorNames(node);
+    const structuredAuthors = extractStructuredAuthors(node);
+    const articleTitle = asString(node?.["article-title"]) ||
+        asString(node?.["chapter-title"]) ||
+        asString(node?.["source-title"]) ||
+        asString(node?.title) ||
+        undefined;
+    const sourceTitle = asString(node?.source) || undefined;
+    const volume = asString(node?.volume) || undefined;
+    const issue = asString(node?.issue) || undefined;
+    const fpage = asString(node?.fpage) || asString(node?.page) || undefined;
+    const lpage = asString(node?.lpage) || undefined;
+    const dateYearStr = asString(node?.year) ||
+        asString(node?.date?.year) ||
+        // Some sources nest pub-date
+        asString((normalizeArray(node?.["pub-date"]) || [])?.[0]?.year) ||
+        undefined;
+    const yearNum = dateYearStr ? parseInt(dateYearStr, 10) : undefined;
+    const year = yearNum && !isNaN(yearNum) ? yearNum : undefined;
+    // Build formatted string (preserving existing logic)
+    const parts = [];
+    if (authorNames.length)
+        parts.push(joinAuthors(authorNames));
+    if (articleTitle)
+        parts.push(ensurePeriod(articleTitle));
+    if (sourceTitle)
+        parts.push(ensurePeriod(sourceTitle));
+    const volIss = [];
+    if (volume)
+        volIss.push(volume);
+    if (issue)
+        volIss.push(`(${issue})`);
+    if (volIss.length)
+        parts.push(volIss.join(" "));
+    const pages = lpage && fpage ? `${fpage}–${lpage}` : fpage || undefined;
+    if (pages)
+        parts.push(pages);
+    if (dateYearStr)
+        parts.push(`(${dateYearStr}).`);
+    const joined = parts.join(" ");
+    const formatted = cleanupCitationText(joined) || undefined;
+    return {
+        formatted,
+        articleTitle,
+        sourceTitle,
+        year,
+        volume,
+        issue,
+        fpage,
+        lpage,
+        authors: structuredAuthors.length ? structuredAuthors : undefined,
+    };
+}
+function joinAuthors(names) {
+    const withDots = names.map((n) => (n.endsWith(".") ? n : n + "."));
+    return withDots.length === 1 ? withDots[0] : withDots.join(", ");
+}
+function ensurePeriod(s) {
+    const t = (s || "").trim();
+    if (!t)
+        return t;
+    return /[.!?]$/.test(t) ? t : t + ".";
+}
+function excludeKeys(obj, keys) {
+    if (!obj || typeof obj !== "object")
+        return obj;
+    const out = Array.isArray(obj) ? [] : {};
+    for (const k of Object.keys(obj)) {
+        if (keys.includes(k))
+            continue;
+        const v = obj[k];
+        if (Array.isArray(v))
+            out[k] = v.map((it) => excludeKeys(it, keys));
+        else if (v && typeof v === "object")
+            out[k] = excludeKeys(v, keys);
+        else
+            out[k] = v;
+    }
+    return out;
+}
+function formatNameNode(n) {
+    if (!n)
+        return undefined;
+    const surname = asString(n?.surname) || asString(n?.["last-name"]) || undefined;
+    const given = asString(n?.["given-names"]) || asString(n?.["first-name"]) || undefined;
+    const full = !surname && !given ? getText(n) : undefined;
+    if (full)
+        return full.trim();
+    if (!surname && !given)
+        return undefined;
+    return [surname, given].filter(Boolean).join(" ");
+}
+function extractAuthorNames(node) {
+    const out = [];
+    // Person-group (author)
+    for (const pg of normalizeArray(node?.["person-group"])) {
+        const type = asString(pg?.["@_person-group-type"]) || "";
+        if (type && type.toLowerCase() !== "author")
+            continue;
+        for (const nm of normalizeArray(pg?.name).concat(normalizeArray(pg?.["string-name"]))) {
+            const formatted = formatNameNode(nm);
+            if (formatted)
+                out.push(formatted);
+        }
+        for (const collab of normalizeArray(pg?.collab)) {
+            const s = getText(collab);
+            if (s)
+                out.push(s);
+        }
+    }
+    // Fallback: direct names under the node
+    for (const nm of normalizeArray(node?.name).concat(normalizeArray(node?.["string-name"]))) {
+        const formatted = formatNameNode(nm);
+        if (formatted)
+            out.push(formatted);
+    }
+    // If still empty, try any contrib-like structure
+    for (const c of normalizeArray(node?.contrib)) {
+        const formatted = formatNameNode(c?.name || c?.["string-name"] || c);
+        if (formatted)
+            out.push(formatted);
+    }
+    return out;
+}
+function parseNameNodeStructured(n) {
+    if (!n)
+        return undefined;
+    const surname = asString(n?.surname) || asString(n?.["last-name"]) || undefined;
+    const givenNames = asString(n?.["given-names"]) || asString(n?.["first-name"]) || undefined;
+    if (!surname && !givenNames)
+        return undefined;
+    return {
+        ...(surname && { surname }),
+        ...(givenNames && { givenNames }),
+    };
+}
+function extractStructuredAuthors(node) {
+    const out = [];
+    for (const pg of normalizeArray(node?.["person-group"])) {
+        const type = asString(pg?.["@_person-group-type"]) || "";
+        if (type && type.toLowerCase() !== "author")
+            continue;
+        for (const nm of normalizeArray(pg?.name).concat(normalizeArray(pg?.["string-name"]))) {
+            const parsed = parseNameNodeStructured(nm);
+            if (parsed)
+                out.push(parsed);
+        }
+    }
+    if (!out.length) {
+        for (const nm of normalizeArray(node?.name).concat(normalizeArray(node?.["string-name"]))) {
+            const parsed = parseNameNodeStructured(nm);
+            if (parsed)
+                out.push(parsed);
+        }
+    }
+    return out;
+}
+function extractPubIds(node) {
+    const ids = {};
+    for (const pid of normalizeArray(node?.["pub-id"])) {
+        const type = (asString(pid?.["@_pub-id-type"]) || "").toLowerCase();
+        const val = asString(pid) || getText(pid) || undefined;
+        if (!val)
+            continue;
+        if (type === "doi")
+            ids.doi = val.trim();
+        else if (type === "pmid")
+            ids.pmid = val.trim();
+        else if (type === "pmc" || type === "pmcid")
+            ids.pmcid = val.trim();
+    }
+    if (!ids.doi) {
+        for (const el of normalizeArray(node?.["ext-link"])) {
+            const type = (asString(el?.["@_ext-link-type"]) || "").toLowerCase();
+            if (type === "doi") {
+                const val = asString(el) || getText(el) || undefined;
+                if (val)
+                    ids.doi = val.trim();
+                break;
+            }
+        }
+    }
+    return ids;
+}
+export function collectReferences(back, domPO) {
+    const lists = normalizeArray(back?.["ref-list"]);
+    const refs = lists.flatMap((l) => normalizeArray(l?.ref));
+    const out = [];
+    for (const r of refs) {
+        const id = asString(r?.["@_id"]) || asString(r?.id) || undefined;
+        const label = getText(r?.label) || undefined;
+        // Prefer structured nodes if present; else fall back to formatting the <ref> while excluding <label>
+        const citationNode = r?.["mixed-citation"] ||
+            r?.["element-citation"] ||
+            r?.["citation"] ||
+            r?.["nlm-citation"] ||
+            undefined;
+        const sourceNode = citationNode || excludeKeys(r, ["label", "@_id", "id"]);
+        const parsed = parseCitationNode(sourceNode);
+        let raw = parsed?.formatted;
+        if (!raw) {
+            raw =
+                getText(r?.["mixed-citation"]) ||
+                    getText(r?.["element-citation"]) ||
+                    getText(r?.["citation"]) ||
+                    getText(r?.["nlm-citation"]) ||
+                    getText(r) ||
+                    undefined;
+            if (raw)
+                raw = cleanupCitationText(raw);
+        }
+        // Extract pub-ids (DOI/PMID/PMCID) and publication type
+        const pubIds = extractPubIds(citationNode || r);
+        const pubType = asString(citationNode?.["@_publication-type"]) || undefined;
+        // Extract text/xml/xml_minimal using preserveOrder when possible
+        let text;
+        let xml;
+        let xml_minimal;
+        if (domPO) {
+            const backPO = poFindFirstByLocal(domPO, "back");
+            if (backPO) {
+                // Try to find a matching <ref> by id and serialize its citation child
+                const refPO = id
+                    ? poFindFirstByLocalAttr(backPO, "ref", "id", id) ||
+                        poFindFirstByLocalAttr(backPO, "ref", "hwp:id", id)
+                    : undefined;
+                const citPO = refPO
+                    ? ["mixed-citation", "element-citation", "citation", "nlm-citation"]
+                        .map((nm) => poFindFirstByLocal(refPO, nm))
+                        .find(Boolean)
+                    : undefined;
+                const target = citPO || refPO;
+                if (target) {
+                    const t = poText(poChildren(target)) || poText(target);
+                    if (t && t.trim())
+                        text = t.trim();
+                    const x = poSerialize(target);
+                    if (x && x.trim())
+                        xml = x;
+                    const xm = poSerializeCitationMinimal(target);
+                    if (xm && xm.trim())
+                        xml_minimal = xm;
+                }
+            }
+        }
+        // Fallback if PO unavailable: synthesize from object-mode text
+        if (!text) {
+            const refObj = citationNode || r;
+            text = getText(refObj) || undefined;
+            if (text && text.trim()) {
+                const escaped = escapeXml(text);
+                xml = `<citation>${escaped}</citation>`;
+                xml_minimal =
+                    serializeCitationMinimalFromObject(refObj) ||
+                        `<citation>${escaped}</citation>`;
+            }
+        }
+        out.push({
+            id,
+            label,
+            raw,
+            text,
+            xml,
+            xml_minimal,
+            articleTitle: parsed?.articleTitle,
+            sourceTitle: parsed?.sourceTitle,
+            year: parsed?.year,
+            volume: parsed?.volume,
+            issue: parsed?.issue,
+            fpage: parsed?.fpage,
+            lpage: parsed?.lpage,
+            doi: pubIds.doi,
+            pmid: pubIds.pmid,
+            pmcid: pubIds.pmcid,
+            authors: parsed?.authors,
+            pubType,
+        });
+    }
+    return out;
+}
+// --------------- flattened paragraphs ---------------
+export function cleanupReferenceText(s) {
+    if (!s)
+        return s;
+    let out = s;
+    out = out.replace(/\s+/g, " ");
+    out = out.replace(/\s+([,;:.!?\)\]\}])/g, "$1");
+    out = out.replace(/([\(\[\{])\s+/g, "$1");
+    out = out.replace(/([,.])(\S)/g, "$1 $2");
+    out = out.replace(/\s*[–-]\s*/g, "–");
+    out = out.replace(/([.!?]){2,}$/g, "$1");
+    return out.trim();
+}
+//# sourceMappingURL=references.js.map

package/dist/normalization/jats/utils/references.js.map

@@ -0,0 +1 @@
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package/dist/normalization/jats/utils/strings.d.ts

@@ -0,0 +1,8 @@
+export declare function normalizeArray<T>(x: T | T[] | undefined | null): T[];
+export declare function asString(x: any): string | undefined;
+export declare function decodeEntities(s: string): string;
+export declare function escapeXml(s: string): string;
+export declare function stripDiacritics(s: string): string;
+export declare function cleanHeading(x?: string): string | undefined;
+export declare function extractEmail(text?: string): string | undefined;
+//# sourceMappingURL=strings.d.ts.map

package/dist/normalization/jats/utils/strings.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"strings.d.ts","sourceRoot":"","sources":["../../../../src/normalization/jats/utils/strings.ts"],"names":[],"mappings":"AAuHA,wBAAgB,cAAc,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,GAAG,SAAS,GAAG,IAAI,GAAG,CAAC,EAAE,CAGpE;AAED,wBAAgB,QAAQ,CAAC,CAAC,EAAE,GAAG,GAAG,MAAM,GAAG,SAAS,CAMnD;AAED,wBAAgB,cAAc,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CA2BhD;AAED,wBAAgB,SAAS,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAO3C;AAED,wBAAgB,eAAe,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAEjD;AAED,wBAAgB,YAAY,CAAC,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAU3D;AAED,wBAAgB,YAAY,CAAC,IAAI,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAI9D"}

package/dist/normalization/jats/utils/strings.js

@@ -0,0 +1,197 @@
+const NAMED_ENTITIES = {
+    amp: "&",
+    lt: "<",
+    gt: ">",
+    quot: '"',
+    apos: "'",
+    nbsp: " ",
+    ndash: "–",
+    mdash: "—",
+    rsquo: "’",
+    lsquo: "‘",
+    rdquo: "”",
+    ldquo: "“",
+    hellip: "…",
+    middot: "·",
+    bull: "•",
+    deg: "°",
+    plusmn: "±",
+    pm: "±",
+    minus: "−",
+    times: "×",
+    divide: "÷",
+    micro: "µ",
+    alpha: "α",
+    beta: "β",
+    gamma: "γ",
+    delta: "δ",
+    epsilon: "ε",
+    zeta: "ζ",
+    eta: "η",
+    theta: "θ",
+    iota: "ι",
+    kappa: "κ",
+    lambda: "λ",
+    mu: "μ",
+    nu: "ν",
+    xi: "ξ",
+    omicron: "ο",
+    pi: "π",
+    rho: "ρ",
+    sigma: "σ",
+    tau: "τ",
+    upsilon: "υ",
+    phi: "φ",
+    chi: "χ",
+    psi: "ψ",
+    omega: "ω",
+    Alpha: "Α",
+    Beta: "Β",
+    Gamma: "Γ",
+    Delta: "Δ",
+    Epsilon: "Ε",
+    Zeta: "Ζ",
+    Eta: "Η",
+    Theta: "Θ",
+    Iota: "Ι",
+    Kappa: "Κ",
+    Lambda: "Λ",
+    Mu: "Μ",
+    Nu: "Ν",
+    Xi: "Ξ",
+    Omicron: "Ο",
+    Pi: "Π",
+    Rho: "Ρ",
+    Sigma: "Σ",
+    Tau: "Τ",
+    Upsilon: "Υ",
+    Phi: "Φ",
+    Chi: "Χ",
+    Psi: "Ψ",
+    Omega: "Ω",
+    le: "≤",
+    ge: "≥",
+    ne: "≠",
+    approx: "≈",
+    equiv: "≡",
+    infin: "∞",
+    laquo: "«",
+    raquo: "»",
+    copy: "©",
+    reg: "®",
+    trade: "™",
+    sect: "§",
+    para: "¶",
+    oe: "œ",
+    OE: "Œ",
+    ae: "æ",
+    AE: "Æ",
+    ntilde: "ñ",
+    Ntilde: "Ñ",
+    eacute: "é",
+    Eacute: "É",
+    aacute: "á",
+    Aacute: "Á",
+    oacute: "ó",
+    Oacute: "Ó",
+    uacute: "ú",
+    Uacute: "Ú",
+    agrave: "à",
+    Agrave: "À",
+    egrave: "è",
+    Egrave: "È",
+    igrave: "ì",
+    Igrave: "Ì",
+    ograve: "ò",
+    Ograve: "Ò",
+    ugrave: "ù",
+    Ugrave: "Ù",
+    acirc: "â",
+    ecirc: "ê",
+    icirc: "î",
+    ocirc: "ô",
+    ucirc: "û",
+    Atilde: "Ã",
+    atilde: "ã",
+    Otilde: "Õ",
+    otilde: "õ",
+};
+export function normalizeArray(x) {
+    if (!x)
+        return [];
+    return Array.isArray(x) ? x : [x];
+}
+export function asString(x) {
+    if (x == null)
+        return undefined;
+    if (typeof x === "string")
+        return x;
+    if (typeof x === "number")
+        return String(x);
+    if (typeof x === "object")
+        return asString(x["#text"]) ?? undefined;
+    return undefined;
+}
+export function decodeEntities(s) {
+    // numeric hex and decimal entities
+    s = s.replace(/&#x([0-9a-fA-F]+);/g, (_, hex) => {
+        const code = parseInt(hex, 16);
+        if (!Number.isFinite(code))
+            return _;
+        try {
+            return String.fromCodePoint(code);
+        }
+        catch {
+            return _;
+        }
+    });
+    s = s.replace(/&#([0-9]+);/g, (_, dec) => {
+        const code = parseInt(dec, 10);
+        if (!Number.isFinite(code))
+            return _;
+        try {
+            return String.fromCodePoint(code);
+        }
+        catch {
+            return _;
+        }
+    });
+    // Named entities
+    s = s.replace(/&([a-zA-Z][a-zA-Z0-9]+);/g, (m, name) => {
+        const rep = NAMED_ENTITIES[name];
+        if (rep != null)
+            return rep;
+        return m;
+    });
+    return s;
+}
+export function escapeXml(s) {
+    return s
+        .replace(/&/g, "&amp;")
+        .replace(/</g, "&lt;")
+        .replace(/>/g, "&gt;")
+        .replace(/"/g, "&quot;")
+        .replace(/'/g, "&apos;");
+}
+export function stripDiacritics(s) {
+    return s.normalize("NFD").replace(/[\u0300-\u036f]/g, "");
+}
+export function cleanHeading(x) {
+    if (!x)
+        return undefined;
+    let s = String(x).trim();
+    // Strip numbering like "1.", "1)", "I.", "A)", etc.
+    s = s.replace(/^\s*([0-9]+|[ivxlcdmIVXLCDM]+|[A-Z])\s*[\.\)\-:]\s*/, "");
+    s = s.replace(/\s+/g, " ").trim();
+    s = stripDiacritics(s.toLowerCase());
+    // Remove trailing punctuation
+    s = s.replace(/[\.:;,-]+$/, "").trim();
+    return s || undefined;
+}
+export function extractEmail(text) {
+    if (!text)
+        return undefined;
+    const m = text.match(/[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,}/i);
+    return m ? m[0] : undefined;
+}
+//# sourceMappingURL=strings.js.map

package/dist/normalization/jats/utils/strings.js.map

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