@mantra-ai/core 0.1.0

package/dist/normalization/jats/utils/build/flatten.js

@@ -0,0 +1,502 @@
+import { createHash } from "node:crypto";
+import { XMLParser } from "fast-xml-parser";
+function toAnchor(s) {
+    return s
+        .toLowerCase()
+        .normalize("NFD")
+        .replace(/[\u0300-\u036f]/g, "")
+        .replace(/[^a-z0-9\s-]/g, "")
+        .trim()
+        .replace(/\s+/g, "-")
+        .replace(/-+/g, "-");
+}
+function toPathAnchor(path) {
+    return path
+        .map((p) => (p.anchor || "").trim())
+        .filter(Boolean)
+        .join("/");
+}
+export function flattenSectionsToBlocks(sections, opts) {
+    const out = [];
+    let order = 0;
+    // Stable stringify to ensure deterministic hashing
+    const stableStringify = (value) => {
+        if (value === null || typeof value !== "object") {
+            return JSON.stringify(value);
+        }
+        if (Array.isArray(value)) {
+            return `[${value.map((v) => stableStringify(v)).join(",")}]`;
+        }
+        const keys = Object.keys(value)
+            .filter((k) => value[k] !== undefined)
+            .sort();
+        return `{${keys
+            .map((k) => `${JSON.stringify(k)}:${stableStringify(value[k])}`)
+            .join(",")}}`;
+    };
+    const computeBlockId = (canonical) => {
+        const canonicalString = stableStringify(canonical);
+        const full = createHash("sha256").update(canonicalString).digest(); // 32 bytes
+        // Take first 8 bytes => 64 bits; map to 16-digit decimal (zero-padded)
+        const first8 = full.subarray(0, 8);
+        let n = 0n;
+        for (const byte of first8)
+            n = (n << 8n) | BigInt(byte);
+        const mod = 10000000000000000n; // 10^16
+        const dec = n % mod;
+        const digits = dec.toString().padStart(16, "0");
+        return `b${digits}`;
+    };
+    const getFigureNumber = (id, label) => {
+        // Prefer label like "Figure 1" -> 1
+        if (label) {
+            const m = label.match(/figure\s*(\d+)/i);
+            if (m && m[1]) {
+                const n = Number(m[1]);
+                if (Number.isFinite(n))
+                    return n;
+            }
+        }
+        // Fallback to id like fig1 -> 1; F12 -> 12; F1a -> 1
+        if (id) {
+            const m = id.match(/(?:fig|f)?\s*(\d+)/i);
+            if (m && m[1]) {
+                const n = Number(m[1]);
+                if (Number.isFinite(n))
+                    return n;
+            }
+        }
+        return undefined;
+    };
+    const buildFigureLinks = (figure) => {
+        // Use the same XML link for both link.xml and as the base for image construction
+        const xmlLink = opts?.sourceUrl;
+        const num = getFigureNumber(figure?.id, figure?.label);
+        if (!xmlLink)
+            return undefined;
+        try {
+            const u = new URL(xmlLink);
+            let path = u.pathname;
+            let imagePath;
+            if (num !== undefined) {
+                if (/\.source\.xml$/i.test(path)) {
+                    imagePath = path.replace(/\.source\.xml$/i, `/F${num}.large.jpg`);
+                }
+                else if (/\.full\.xml$/i.test(path)) {
+                    imagePath = path.replace(/\.full\.xml$/i, `/F${num}.large.jpg`);
+                }
+            }
+            const imageUrl = imagePath
+                ? `${u.origin}${imagePath}${u.search || ""}${u.hash || ""}`
+                : undefined;
+            return {
+                xml: u.toString(),
+                ...(imageUrl ? { image_large_jpg: imageUrl } : {}),
+            };
+        }
+        catch {
+            return { xml: xmlLink };
+        }
+    };
+    const getTableNumber = (id, label) => {
+        // Prefer label like "Table 1" -> 1
+        if (label) {
+            const m = label.match(/table\s*(\d+)/i);
+            if (m && m[1]) {
+                const n = Number(m[1]);
+                if (Number.isFinite(n))
+                    return n;
+            }
+        }
+        // Fallback to id like table1|tbl1|t1 -> 1
+        if (id) {
+            const m = id.match(/(?:table|tbl|t)?\s*(\d+)/i);
+            if (m && m[1]) {
+                const n = Number(m[1]);
+                if (Number.isFinite(n))
+                    return n;
+            }
+        }
+        return undefined;
+    };
+    const buildTableLinks = (table) => {
+        const xmlLink = opts?.sourceUrl;
+        const num = getTableNumber(table?.id, table?.label);
+        if (!xmlLink)
+            return undefined;
+        try {
+            const u = new URL(xmlLink);
+            let path = u.pathname;
+            let imagePath;
+            if (num !== undefined) {
+                if (/\.source\.xml$/i.test(path)) {
+                    imagePath = path.replace(/\.source\.xml$/i, `/T${num}.medium.gif`);
+                }
+                else if (/\.full\.xml$/i.test(path)) {
+                    imagePath = path.replace(/\.full\.xml$/i, `/T${num}.medium.gif`);
+                }
+            }
+            const imageUrl = imagePath
+                ? `${u.origin}${imagePath}${u.search || ""}${u.hash || ""}`
+                : undefined;
+            return {
+                xml: u.toString(),
+                ...(imageUrl ? { image_medium_gif: imageUrl } : {}),
+            };
+        }
+        catch {
+            return { xml: xmlLink };
+        }
+    };
+    const parseAttrs = (attrStr) => {
+        const attrs = {};
+        const re = /(\w[\w:-]*)\s*=\s*"([^"]*)"/g;
+        let m;
+        while ((m = re.exec(attrStr)))
+            attrs[m[1]] = m[2];
+        return attrs;
+    };
+    const parseMinimalXmlToTextAndXrefs = (xml) => {
+        let out = "";
+        const xrefs = [];
+        let i = 0;
+        const len = xml.length;
+        const readUntil = (ch) => {
+            const j = xml.indexOf(ch, i);
+            const s = j >= 0 ? xml.slice(i, j) : xml.slice(i);
+            i = j >= 0 ? j : len;
+            return s;
+        };
+        while (i < len) {
+            const lt = xml.indexOf("<", i);
+            if (lt < 0) {
+                out += xml.slice(i);
+                break;
+            }
+            // Text before tag
+            if (lt > i) {
+                out += xml.slice(i, lt);
+                i = lt;
+            }
+            // At a tag
+            const gt = xml.indexOf(">", i + 1);
+            if (gt < 0)
+                break; // malformed
+            const tagInner = xml.slice(i + 1, gt);
+            const isClosing = tagInner.startsWith("/");
+            const selfClosing = tagInner.endsWith("/");
+            const token = isClosing ? tagInner.slice(1).trim() : tagInner.trim();
+            const nameMatch = token.match(/^[a-zA-Z][a-zA-Z0-9_-]*/);
+            const name = nameMatch ? nameMatch[0].toLowerCase() : "";
+            const attrStr = token.slice(name.length).trim();
+            i = gt + 1;
+            if (isClosing || selfClosing)
+                continue; // no content to consume
+            // Handle known xref-like tags by consuming until closing tag
+            const typeMap = {
+                bibliography: "citation",
+                figure: "figure-ref",
+                table: "table-ref",
+                supplementary: "supplementary-ref",
+                extlink: "extlink",
+            };
+            const typ = typeMap[name];
+            if (!typ)
+                continue;
+            const closeTag = `</${name}>`;
+            const closeIdx = xml.indexOf(closeTag, i);
+            let innerRaw;
+            if (closeIdx >= 0) {
+                innerRaw = xml.slice(i, closeIdx);
+            }
+            else {
+                innerRaw = "";
+            }
+            // Remove any nested tags inside inner text
+            const innerText = innerRaw.replace(/<[^>]+>/g, "");
+            // Build xref item with span in out
+            const start = out.length;
+            out += innerText;
+            const end = out.length;
+            const attrs = parseAttrs(attrStr);
+            const item = {
+                type: typ,
+                label: innerText,
+                span: [start, end],
+            };
+            if (typ === "extlink")
+                item.target_id = attrs.href || attrs["xlink:href"];
+            else
+                item.target_id = attrs.target || attrs.rid;
+            xrefs.push(item);
+            // Advance past closing tag if present
+            if (closeIdx >= 0)
+                i = closeIdx + closeTag.length;
+        }
+        return { text: out, xrefs };
+    };
+    const walk = (s, depth, path, usedIds) => {
+        const leafAnchor = toAnchor(s.title || s.normalized_title || s.category || "section");
+        const ancestors = path.map((p) => p.anchor ||
+            toAnchor(p.title || p.normalized_title || p.category || "section"));
+        const path_anchor = toPathAnchor([...ancestors, leafAnchor].map((a) => ({ anchor: a })));
+        // Compute or synthesize a section id consistent with summary
+        const sourceSid = s.id;
+        const base = sourceSid?.trim() || `sec_${leafAnchor}`;
+        let sid = base;
+        let i = 1;
+        while (usedIds.has(sid))
+            sid = `${base}_${i++}`;
+        usedIds.add(sid);
+        const baseMeta = {
+            section_id: sid,
+            path_anchor,
+            // order and index_in_section set per block below
+        };
+        let indexInSection = 0;
+        const blocks = s.blocks || [];
+        const selfNode = {
+            anchor: leafAnchor,
+            category: s.category || "other",
+            normalized_title: s.normalized_title,
+            title: s.title,
+            sid,
+        };
+        for (const b of blocks) {
+            if (b.kind === "paragraph") {
+                let paraText = b.text;
+                let xrefs;
+                if (b.xml_minimal) {
+                    const parsed = parseMinimalXmlToTextAndXrefs(b.xml_minimal);
+                    // Prefer reconstructed text for alignment
+                    if (parsed.text && parsed.text.trim())
+                        paraText = parsed.text;
+                    if (parsed.xrefs && parsed.xrefs.length)
+                        xrefs = parsed.xrefs;
+                }
+                const canonical = {
+                    kind: "paragraph",
+                    section_id: baseMeta.section_id,
+                    path_anchor: baseMeta.path_anchor,
+                    index_in_section: indexInSection,
+                    plain_text: paraText,
+                    ...(b.xml ? { raw_xml: b.xml } : {}),
+                    ...(b.xml_minimal ? { minimal_xml: b.xml_minimal } : {}),
+                };
+                const block_id = computeBlockId(canonical);
+                out.push({
+                    kind: "paragraph",
+                    order: order++,
+                    index_in_section: indexInSection++,
+                    block_id,
+                    plain_text: paraText,
+                    ...(b.xml ? { raw_xml: b.xml } : {}),
+                    ...(b.xml_minimal ? { minimal_xml: b.xml_minimal } : {}),
+                    ...(xrefs ? { xrefs } : {}),
+                    ...baseMeta,
+                });
+            }
+            else if (b.kind === "figure") {
+                const capParas = Array.isArray(b?.caption?.paragraphs)
+                    ? b.caption.paragraphs
+                    : [];
+                let capPlain = capParas
+                    .map((p) => String(p).trim())
+                    .filter(Boolean)
+                    .join(" ")
+                    .trim();
+                const capXmlArr = Array.isArray(b?.caption?.xml)
+                    ? b.caption.xml
+                    : [];
+                let capXml = capXmlArr
+                    .map((x) => String(x).trim())
+                    .filter(Boolean)
+                    .join("\n");
+                const capMinArr = Array.isArray(b?.caption?.xml_minimal)
+                    ? b.caption.xml_minimal
+                    : [];
+                let capMin = capMinArr
+                    .map((x) => String(x).trim())
+                    .filter(Boolean)
+                    .join("\n");
+                let xrefs;
+                if (capMin) {
+                    const parsed = parseMinimalXmlToTextAndXrefs(capMin);
+                    if (parsed.text && parsed.text.trim())
+                        capPlain = parsed.text;
+                    if (parsed.xrefs && parsed.xrefs.length)
+                        xrefs = parsed.xrefs;
+                }
+                const canonical = {
+                    kind: "figure",
+                    section_id: baseMeta.section_id,
+                    path_anchor: baseMeta.path_anchor,
+                    index_in_section: indexInSection,
+                    id: b.id,
+                    label: b.label,
+                    title: b.title,
+                    ...(capPlain ? { plain_text: capPlain } : {}),
+                    ...(capXml ? { raw_xml: capXml } : {}),
+                    ...(capMin ? { minimal_xml: capMin } : {}),
+                };
+                const block_id = computeBlockId(canonical);
+                out.push({
+                    kind: "figure",
+                    order: order++,
+                    index_in_section: indexInSection++,
+                    block_id,
+                    id: b.id,
+                    label: b.label,
+                    title: b.title,
+                    ...(capPlain ? { plain_text: capPlain } : {}),
+                    ...(capXml ? { raw_xml: capXml } : {}),
+                    ...(capMin ? { minimal_xml: capMin } : {}),
+                    ...(xrefs ? { xrefs } : {}),
+                    ...(buildFigureLinks(b) ? { link: buildFigureLinks(b) } : {}),
+                    ...baseMeta,
+                });
+            }
+            else if (b.kind === "table") {
+                const capParas = Array.isArray(b?.caption?.paragraphs)
+                    ? b.caption.paragraphs
+                    : [];
+                let capPlain = capParas
+                    .map((p) => String(p).trim())
+                    .filter(Boolean)
+                    .join(" ")
+                    .trim();
+                const capXmlArr = Array.isArray(b?.caption?.xml)
+                    ? b.caption.xml
+                    : [];
+                let capXml = capXmlArr
+                    .map((x) => String(x).trim())
+                    .filter(Boolean)
+                    .join("\n");
+                const capMinArr = Array.isArray(b?.caption?.xml_minimal)
+                    ? b.caption.xml_minimal
+                    : [];
+                let capMin = capMinArr
+                    .map((x) => String(x).trim())
+                    .filter(Boolean)
+                    .join("\n");
+                let xrefs;
+                if (capMin) {
+                    const parsed = parseMinimalXmlToTextAndXrefs(capMin);
+                    if (parsed.text && parsed.text.trim())
+                        capPlain = parsed.text;
+                    if (parsed.xrefs && parsed.xrefs.length)
+                        xrefs = parsed.xrefs;
+                }
+                const canonical = {
+                    kind: "table",
+                    section_id: baseMeta.section_id,
+                    path_anchor: baseMeta.path_anchor,
+                    index_in_section: indexInSection,
+                    id: b.id,
+                    label: b.label,
+                    title: b.title,
+                    ...(capPlain ? { plain_text: capPlain } : {}),
+                    ...(capXml ? { raw_xml: capXml } : {}),
+                    ...(capMin ? { minimal_xml: capMin } : {}),
+                };
+                const block_id = computeBlockId(canonical);
+                out.push({
+                    kind: "table",
+                    order: order++,
+                    index_in_section: indexInSection++,
+                    block_id,
+                    id: b.id,
+                    label: b.label,
+                    title: b.title,
+                    ...(capPlain ? { plain_text: capPlain } : {}),
+                    ...(capXml ? { raw_xml: capXml } : {}),
+                    ...(capMin ? { minimal_xml: capMin } : {}),
+                    ...(xrefs ? { xrefs } : {}),
+                    ...(buildTableLinks(b) ? { link: buildTableLinks(b) } : {}),
+                    ...baseMeta,
+                });
+            }
+            else if (b.kind === "section") {
+                // push nothing for the container; recurse
+                const nextPath = path.concat(selfNode);
+                walk(b.section, depth + 1, nextPath, usedIds);
+            }
+        }
+        // Recurse into nested sections listed under Section.sections as well
+        for (const sub of s.sections || []) {
+            const nextPath = path.concat(selfNode);
+            walk(sub, depth + 1, nextPath, usedIds);
+        }
+    };
+    {
+        const usedIds = new Set();
+        for (const s of sections) {
+            const rootPath = [];
+            walk(s, 0, rootPath, usedIds);
+        }
+    }
+    return out;
+}
+export function flattenSectionsToSummary(sections) {
+    const out = [];
+    let order = 0;
+    const seen = new Set();
+    const usedIds = new Set();
+    const walk = (s, depth, path) => {
+        if (seen.has(s))
+            return; // avoid double-visiting same section
+        seen.add(s);
+        const anchor = toAnchor(s.title || s.normalized_title || s.category || "section");
+        const ancestors = path.map((p) => p.anchor ||
+            toAnchor(p.title || p.normalized_title || p.category || "section"));
+        const top = path.length
+            ? path[0]
+            : {
+                normalized_title: s.normalized_title,
+                title: s.title,
+                category: s.category,
+            };
+        // Prefer source id; otherwise synthesize a stable-ish id from anchor.
+        // Always deduplicate — even source ids can collide across nested sections.
+        const sourceSid = s.id;
+        const base = sourceSid?.trim() || `sec_${anchor}`;
+        let sid = base;
+        let i = 1;
+        while (usedIds.has(sid))
+            sid = `${base}_${i++}`;
+        usedIds.add(sid);
+        out.push({
+            id: sid,
+            title: s.title,
+            normalized_title: s.normalized_title,
+            category: s.category,
+            level: depth + 1,
+            order: order++,
+            anchor,
+            ...(ancestors.length ? { path_anchors: ancestors } : {}),
+            path_anchor: toPathAnchor([...ancestors, anchor].map((a) => ({ anchor: a }))),
+            top_normalized_title: top.normalized_title || s.normalized_title,
+        });
+        // Recurse into blocks that are sections (interleaved) to preserve order
+        const blocks = s.blocks || [];
+        const selfNode = {
+            anchor,
+            normalized_title: s.normalized_title,
+            title: s.title,
+            category: s.category,
+        };
+        for (const b of blocks) {
+            if (b.kind === "section" && b.section) {
+                walk(b.section, depth + 1, path.concat(selfNode));
+            }
+        }
+        // Also walk any trailing nested sections listed under Section.sections
+        for (const sub of s.sections || []) {
+            walk(sub, depth + 1, path.concat(selfNode));
+        }
+    };
+    for (const s of sections)
+        walk(s, 0, []);
+    return out;
+}
+//# sourceMappingURL=flatten.js.map

package/dist/normalization/jats/utils/build/flatten.js.map

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

@@ -0,0 +1,10 @@
+import type { NormalizedJats } from "../types";
+export declare function buildMetaAbstract(n: NormalizedJats): {
+    abstract?: {
+        paragraphs?: string[];
+        xml?: string[];
+        xml_minimal?: string[];
+        title?: string;
+    };
+};
+//# sourceMappingURL=meta.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"meta.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/build/meta.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,UAAU,CAAC;AAE/C,wBAAgB,iBAAiB,CAAC,CAAC,EAAE,cAAc,GAAG;IACpD,QAAQ,CAAC,EAAE;QACT,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;QACtB,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC;QACf,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;CACH,CAwBA"}

package/dist/normalization/jats/utils/build/meta.js

@@ -0,0 +1,32 @@
+export function buildMetaAbstract(n) {
+    const abstracts = (n.abstracts || []);
+    if (!abstracts.length)
+        return {};
+    const firstWithBlocks = abstracts.find((a) => Array.isArray(a.blocks) && a.blocks.length);
+    const first = firstWithBlocks || abstracts[0];
+    const paragraphs = [];
+    const xml = [];
+    const xml_minimal = [];
+    const blocks = (first.blocks || []);
+    for (const b of blocks) {
+        if (b.kind === "paragraph") {
+            if (b.text)
+                paragraphs.push(b.text);
+            if (b.xml)
+                xml.push(b.xml);
+            if (b.xml_minimal)
+                xml_minimal.push(b.xml_minimal);
+        }
+    }
+    const abstract = {};
+    if (paragraphs.length)
+        abstract.paragraphs = paragraphs;
+    if (xml.length)
+        abstract.xml = xml;
+    if (xml_minimal.length)
+        abstract.xml_minimal = xml_minimal;
+    if (first.title)
+        abstract.title = first.title;
+    return Object.keys(abstract).length ? { abstract } : {};
+}
+//# sourceMappingURL=meta.js.map

package/dist/normalization/jats/utils/build/meta.js.map

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

@@ -0,0 +1,3 @@
+import type { BuildOptions } from "../types";
+export declare function buildNormalizerVersion(env?: BuildOptions["normalizerVersion"]): string;
+//# sourceMappingURL=version.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"version.d.ts","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/build/version.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,UAAU,CAAC;AAE7C,wBAAgB,sBAAsB,CACpC,GAAG,CAAC,EAAE,YAAY,CAAC,mBAAmB,CAAC,GACtC,MAAM,CAUR"}

package/dist/normalization/jats/utils/build/version.js

@@ -0,0 +1,11 @@
+export function buildNormalizerVersion(env) {
+    const sha = process.env.REVENG_GIT_SHA ||
+        process.env.GIT_COMMIT_SHA ||
+        process.env.VERCEL_GIT_COMMIT_SHA ||
+        process.env.SOURCE_VERSION ||
+        "unknown";
+    const shortSha = /^[a-f0-9]{7,40}$/i.test(sha) ? sha.slice(0, 7) : sha;
+    const ver = env || process.env.REVENG_NORMALIZER_VERSION || "0.0.0";
+    return `reveng-xml-normalizer@${ver}+git:${shortSha}`;
+}
+//# sourceMappingURL=version.js.map

package/dist/normalization/jats/utils/build/version.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../../../../../src/normalization/jats/utils/build/version.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,sBAAsB,CACpC,GAAuC;IAEvC,MAAM,GAAG,GACP,OAAO,CAAC,GAAG,CAAC,cAAc;QAC1B,OAAO,CAAC,GAAG,CAAC,cAAc;QAC1B,OAAO,CAAC,GAAG,CAAC,qBAAqB;QACjC,OAAO,CAAC,GAAG,CAAC,cAAc;QAC1B,SAAS,CAAC;IACZ,MAAM,QAAQ,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;IACvE,MAAM,GAAG,GAAG,GAAG,IAAI,OAAO,CAAC,GAAG,CAAC,yBAAyB,IAAI,OAAO,CAAC;IACpE,OAAO,yBAAyB,GAAG,QAAQ,QAAQ,EAAE,CAAC;AACxD,CAAC"}

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

@@ -0,0 +1,11 @@
+import type { SectionCategory } from "./types";
+export declare function categoryFromSecType(secType?: string): SectionCategory | undefined;
+export declare function categoryFromDirectHeading(t: string): SectionCategory | undefined;
+export declare function categoryFromKeywords(t: string): SectionCategory | undefined;
+export declare function classifySection(rawTitle: string | undefined, secType: string | undefined, level: number, parentCategory: SectionCategory | undefined): {
+    category: SectionCategory;
+    normalized_title: string | undefined;
+};
+export declare function normalizedTitleFor(cat: SectionCategory): string;
+export declare const BACK_MATTER_CATEGORIES: SectionCategory[];
+//# sourceMappingURL=category.d.ts.map

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

@@ -0,0 +1 @@
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