@mantra-ai/core 0.1.0

package/dist/normalization/jats/normalize.js

@@ -0,0 +1,213 @@
+import { XMLParser } from "fast-xml-parser";
+import { asString } from "./utils/strings";
+import { collectReferences } from "./utils/references";
+import { poFindFirstByLocal, poFindDescendantsByLocal } from "./utils/po/query";
+import { poChildren } from "./utils/po/nodes";
+import { finalizeNormalizedJats } from "./utils/build/finalize";
+import { collectSections, collectSectionNode, collectLooseBodyParagraphsFromPORoot, } from "./utils/collectors/sections";
+import { collectAbstracts } from "./utils/collectors/abstracts";
+import { collectAckRich, collectNotesRich, collectSupplementary, collectBackSecRich, collectGenericBackSections, } from "./utils/collectors/back";
+import { collectContributors, collectAffiliations, } from "./utils/collectors/contributors";
+import { collectKeywords } from "./utils/collectors/keywords";
+import { collectIds, collectJournal, collectPubDates, collectLicense, } from "./utils/collectors/meta";
+import { getBodyNode, pickNs, getText, nsArray } from "./utils/xml";
+import { poText } from "./utils/po/text";
+/**
+ * Entry point: normalize a JATS XML string to a simple domain JSON.
+ **/
+export function normalizeJatsXml(xml) {
+    const parser = new XMLParser({
+        ignoreAttributes: false,
+        attributeNamePrefix: "@_",
+        textNodeName: "#text",
+        // Keep order is not required for this minimal version
+    });
+    // A secondary parser in preserveOrder mode for ordered text extraction in limited paths
+    const poParser = new XMLParser({
+        ignoreAttributes: false,
+        attributeNamePrefix: "@_",
+        textNodeName: "#text",
+        preserveOrder: true,
+    });
+    const domPO = poParser.parse(xml);
+    const dom = parser.parse(xml);
+    const article = dom?.article || pickNs(dom, "article") || {};
+    const front = article?.front || {};
+    const journalMeta = front?.["journal-meta"] || {};
+    const articleMeta = front?.["article-meta"] || {};
+    const body = getBodyNode(article);
+    const back = article?.back || {};
+    const meta = {
+        ids: collectIds(articleMeta),
+        title: getText(articleMeta?.["title-group"]?.["article-title"]),
+        journal: collectJournal(journalMeta),
+        pub_dates: collectPubDates(articleMeta),
+        volume: asString(articleMeta?.volume),
+        issue: asString(articleMeta?.issue),
+        elocation_id: asString(articleMeta?.["elocation-id"]),
+        license: collectLicense(articleMeta, xml, domPO),
+        self_uri: articleMeta?.["self-uri"]?.["@_xlink:href"] ||
+            articleMeta?.["self-uri"]?.["@_href"] ||
+            undefined,
+    };
+    const contributors = collectContributors(articleMeta, back);
+    const affiliations = collectAffiliations(articleMeta);
+    const abstracts = collectAbstracts(articleMeta, domPO);
+    const keywords = collectKeywords(articleMeta);
+    let sections = collectSections(article, body, domPO);
+    const ackRich = collectAckRich(back, domPO);
+    const notesRich = collectNotesRich(back, domPO);
+    const refs = collectReferences(back, domPO);
+    const supplementary = collectSupplementary(body, back);
+    const davRich = collectBackSecRich(back, ["data-availability"], domPO);
+    const fundingRich = collectBackSecRich(back, ["funding"], domPO);
+    // Intentionally do not build supplementary sections here.
+    // Supplementary items (files/figures/tables) will be surfaced under data.supplementary during finalization.
+    // Fallbacks for ultra-minimal or slightly malformed JATS:
+    // 1) If title missing, try to locate <article-title> anywhere (prefer under <front> if present)
+    if (!meta.title) {
+        const frontPO = poFindFirstByLocal(domPO, "front");
+        const titleNode = (frontPO && poFindFirstByLocal(frontPO, "article-title")) ||
+            poFindFirstByLocal(domPO, "article-title");
+        const t = (titleNode && poText(poChildren(titleNode))) ||
+            (titleNode && poText(titleNode));
+        if (t)
+            meta.title = t;
+    }
+    // 2) If no sections and no <body>, attempt to collect top-level paragraphs from a broader scope
+    if (!sections.length) {
+        // Prefer a concrete container if available
+        const bodyPO = getBodyNodePO(domPO);
+        const articlePO = poFindFirstByLocal(domPO, "article");
+        let paras = [];
+        if (bodyPO) {
+            paras = collectLooseBodyParagraphsFromPORoot(bodyPO);
+        }
+        else if (articlePO) {
+            // Some feeds place <p> directly under <article> (or equivalent) without <body>
+            paras = collectLooseBodyParagraphsFromPORoot(articlePO);
+        }
+        else {
+            // Last resort: collect all <p> nodes in the document in order
+            const pNodes = poFindDescendantsByLocal(domPO, "p");
+            const seen = new Set();
+            for (const pn of pNodes) {
+                const txt = poText(poChildren(pn)) || poText(pn);
+                const normalized = (txt || "").trim();
+                if (normalized && !seen.has(normalized)) {
+                    seen.add(normalized);
+                    paras.push(normalized);
+                }
+            }
+        }
+        if (paras.length)
+            sections = [
+                {
+                    normalized_title: "Other",
+                    category: "other",
+                    blocks: paras.map((t) => ({ kind: "paragraph", text: t })),
+                },
+            ];
+    }
+    // Build annex sections blending known buckets and generic back sections
+    const annexSections = [];
+    const pushIfAny = (title, normTitle, category, rich) => {
+        const paras = rich.text || [];
+        const xml = rich.xml || [];
+        const xmlm = rich.xml_minimal || [];
+        if (!paras.length && !xml.length && !xmlm.length)
+            return;
+        const sec = {
+            title: title || normTitle,
+            normalized_title: normTitle,
+            category: category || undefined,
+            blocks: [],
+        };
+        // Build paragraph blocks in order
+        const maxLen = paras.length;
+        for (let i = 0; i < maxLen; i++) {
+            const t = paras[i];
+            const x = xml[i];
+            const xm = xmlm[i];
+            if (!t || !t.trim())
+                continue;
+            sec.blocks.push({
+                kind: "paragraph",
+                text: t.trim(),
+                ...(x ? { xml: x } : {}),
+                ...(xm ? { xml_minimal: xm } : {}),
+            });
+        }
+        if (!sec.blocks?.length)
+            delete sec.blocks;
+        annexSections.push(sec);
+    };
+    pushIfAny(ackRich.title, "Acknowledgements", "acknowledgements", ackRich);
+    pushIfAny(davRich.title, "Data Availability", "data_availability", davRich);
+    pushIfAny(fundingRich.title, "Funding", "funding", fundingRich);
+    pushIfAny(notesRich.title, "Notes", "notes", notesRich);
+    // Do not push supplementary sections into annex sections to avoid duplication.
+    // Generic back <sec> sections via dedicated collector
+    try {
+        const genericBack = collectGenericBackSections(back, domPO);
+        if (genericBack.length)
+            annexSections.push(...genericBack);
+    }
+    catch { }
+    // Build unified content list (abstract(s) + body.sections + annex sections)
+    const unifiedContent = buildUnifiedContent(abstracts, sections, annexSections);
+    return {
+        meta,
+        contributors: contributors.length ? contributors : undefined,
+        affiliations: affiliations.length ? affiliations : undefined,
+        abstracts: abstracts.length ? abstracts : undefined,
+        keywords: keywords.length ? keywords : undefined,
+        content: unifiedContent.length ? unifiedContent : undefined,
+        body: { sections },
+        back: {
+            refs: refs.length ? refs : undefined,
+            supplementary: supplementary.length ? supplementary : undefined,
+            sections: annexSections.length ? annexSections : undefined,
+        },
+    };
+}
+// Convenience wrapper: normalize then finalize to finalized envelope
+export function normalizeJatsToDoc(xml, opts) {
+    const n = normalizeJatsXml(xml);
+    return finalizeNormalizedJats(n, xml, opts);
+}
+// Build a unified, ordered content list composed of:
+// - Abstracts as section(s) with category "abstract"
+// - Body sections
+// - Annex sections
+function buildUnifiedContent(abstracts, bodySections, annexSections) {
+    const out = [];
+    // Abstract(s)
+    for (const a of abstracts || []) {
+        const anyBlocks = a.blocks;
+        const blocks = anyBlocks && anyBlocks.length ? anyBlocks.slice() : [];
+        const absSection = {
+            title: a.title,
+            normalized_title: "Abstract",
+            category: "abstract",
+            ...(blocks.length ? { blocks } : {}),
+        };
+        out.push(absSection);
+    }
+    // Body sections
+    for (const s of bodySections || [])
+        out.push(s);
+    // Annex/back sections
+    for (const s of annexSections || [])
+        out.push(s);
+    return out;
+}
+function getBodyNodePO(domPO) {
+    const article = poFindFirstByLocal(domPO, "article");
+    if (!article)
+        return undefined;
+    const body = poFindFirstByLocal(article, "body") ||
+        poFindFirstByLocal(article, "article-body");
+    return body;
+}
+//# sourceMappingURL=normalize.js.map

package/dist/normalization/jats/normalize.js.map

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package/dist/normalization/jats/utils/build/finalize.d.ts

@@ -0,0 +1,3 @@
+import type { NormalizedJats, BuildOptions, NormalizedDocEnvelope } from "../types";
+export declare function finalizeNormalizedJats(n: NormalizedJats, xml: string, opts?: BuildOptions): NormalizedDocEnvelope;
+//# sourceMappingURL=finalize.d.ts.map

package/dist/normalization/jats/utils/build/finalize.d.ts.map

@@ -0,0 +1 @@
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