@ncukondo/search-hub 0.12.1 → 0.12.2

package/dist/fulltext/convert/jats-parser.js

@@ -1,887 +0,0 @@
-import { XMLParser } from "fast-xml-parser";
-const parser = new XMLParser({
-  ignoreAttributes: false,
-  attributeNamePrefix: "@_",
-  textNodeName: "#text",
-  trimValues: false,
-  preserveOrder: true,
-  processEntities: true,
-  htmlEntities: true
-});
-function getTagName(node) {
-  for (const key of Object.keys(node)) {
-    if (key !== ":@" && key !== "#text") return key;
-  }
-  return void 0;
-}
-function getChildren(node) {
-  const tag = getTagName(node);
-  if (!tag) return [];
-  const children = node[tag];
-  return Array.isArray(children) ? children : [];
-}
-function getAttr(node, attrName) {
-  const attrs = node[":@"];
-  if (!attrs) return void 0;
-  const val = attrs[`@_${attrName}`];
-  return val != null ? String(val) : void 0;
-}
-function getAttrs(node) {
-  const attrs = node[":@"];
-  if (!attrs) return {};
-  const result = {};
-  for (const [key, value] of Object.entries(attrs)) {
-    if (key.startsWith("@_")) {
-      result[key.slice(2)] = String(value);
-    }
-  }
-  return result;
-}
-function findChild(children, tagName) {
-  for (const child of children) {
-    if (tagName in child) {
-      const childArr = child[tagName];
-      return {
-        node: child,
-        children: Array.isArray(childArr) ? childArr : [],
-        attrs: getAttrs(child)
-      };
-    }
-  }
-  return void 0;
-}
-function findChildren(children, tagName) {
-  const results = [];
-  for (const child of children) {
-    if (tagName in child) {
-      const childArr = child[tagName];
-      results.push({
-        node: child,
-        children: Array.isArray(childArr) ? childArr : [],
-        attrs: getAttrs(child)
-      });
-    }
-  }
-  return results;
-}
-function getTextContent(child) {
-  if ("#text" in child) {
-    const val = child["#text"];
-    return val != null ? String(val) : void 0;
-  }
-  return void 0;
-}
-function findArticle(parsed) {
-  const direct = findChild(parsed, "article");
-  if (direct) return direct;
-  const wrapper = findChild(parsed, "pmc-articleset");
-  if (wrapper) return findChild(wrapper.children, "article");
-  return void 0;
-}
-const SPACE_AFTER_TAGS = /* @__PURE__ */ new Set([
-  "surname",
-  "given-names",
-  "name",
-  "string-name"
-]);
-function extractAllText(node) {
-  if (node == null) return "";
-  if (typeof node === "string") return node;
-  if (typeof node === "number") return String(node);
-  if (Array.isArray(node)) {
-    return joinChildTexts(node);
-  }
-  if (typeof node === "object") {
-    const obj = node;
-    const text = getTextContent(obj);
-    if (text != null) return text;
-    const tag = getTagName(obj);
-    if (tag) {
-      const children = obj[tag];
-      if (Array.isArray(children)) {
-        return joinChildTexts(children);
-      }
-    }
-  }
-  return "";
-}
-function joinChildTexts(children) {
-  const parts = [];
-  for (const child of children) {
-    const text = extractAllText(child);
-    if (!text) continue;
-    const tag = getTagName(child);
-    if (tag && SPACE_AFTER_TAGS.has(tag) && parts.length > 0) {
-      const prev = parts[parts.length - 1];
-      if (prev && !/[\s,;.:()\-/]$/.test(prev)) {
-        parts.push(" ");
-      }
-    }
-    parts.push(text);
-  }
-  return parts.join("");
-}
-function parseJatsMetadata(xml) {
-  const parsed = parser.parse(xml);
-  const article = findArticle(parsed);
-  if (!article) return { title: "", authors: [] };
-  const front = findChild(article.children, "front");
-  if (!front) return { title: "", authors: [] };
-  const articleMeta = findChild(front.children, "article-meta");
-  if (!articleMeta) return { title: "", authors: [] };
-  const metaChildren = articleMeta.children;
-  const titleGroup = findChild(metaChildren, "title-group");
-  const articleTitle = titleGroup ? findChild(titleGroup.children, "article-title") : void 0;
-  const title = articleTitle ? extractAllText(articleTitle.children) : "";
-  const articleIds = findChildren(metaChildren, "article-id");
-  let doi;
-  let pmcid;
-  let pmid;
-  for (const idEntry of articleIds) {
-    const idType = idEntry.attrs["pub-id-type"];
-    const idText = extractAllText(idEntry.children);
-    if (idType === "doi") doi = idText;
-    if (idType === "pmc" || idType === "pmcid") {
-      pmcid = idText.replace(/^PMC/, "");
-    }
-    if (idType === "pmid") pmid = idText;
-  }
-  const authors = [];
-  const contribGroup = findChild(metaChildren, "contrib-group");
-  if (contribGroup) {
-    const contribs = findChildren(contribGroup.children, "contrib");
-    for (const contrib of contribs) {
-      if (contrib.attrs["contrib-type"] !== "author") continue;
-      const nameNode = findChild(contrib.children, "name");
-      if (!nameNode) continue;
-      const surnameNode = findChild(nameNode.children, "surname");
-      const givenNamesNode = findChild(nameNode.children, "given-names");
-      const author = {
-        surname: surnameNode ? extractAllText(surnameNode.children) : ""
-      };
-      const givenNames = givenNamesNode ? extractAllText(givenNamesNode.children) : "";
-      if (givenNames) {
-        author.givenNames = givenNames;
-      }
-      authors.push(author);
-    }
-  }
-  const abstractNode = findChild(metaChildren, "abstract");
-  let abstract;
-  if (abstractNode) {
-    const sections = findChildren(abstractNode.children, "sec");
-    if (sections.length > 0) {
-      const parts = [];
-      for (const sec of sections) {
-        const secTitleNode = findChild(sec.children, "title");
-        const secTitle = secTitleNode ? extractAllText(secTitleNode.children) : "";
-        const secPs = findChildren(sec.children, "p");
-        const text = secPs.map((p) => extractAllText(p.children)).join(" ");
-        if (secTitle) {
-          parts.push(`${secTitle}: ${text}`);
-        } else {
-          parts.push(text);
-        }
-      }
-      abstract = parts.join("\n\n");
-    } else {
-      const paragraphs = findChildren(abstractNode.children, "p");
-      if (paragraphs.length > 0) {
-        abstract = paragraphs.map((p) => extractAllText(p.children)).join("\n\n");
-      } else {
-        const text = extractAllText(abstractNode.children);
-        if (text) abstract = text;
-      }
-    }
-  }
-  const pubDates = findChildren(metaChildren, "pub-date");
-  let publicationDate;
-  const datePriority = { epub: 0, ppub: 1, collection: 2 };
-  let bestPriority = Infinity;
-  for (const pd of pubDates) {
-    const dateType = pd.attrs["pub-type"] ?? pd.attrs["date-type"] ?? "";
-    const priority = datePriority[dateType] ?? 3;
-    if (priority < bestPriority) {
-      bestPriority = priority;
-      const yearNode = findChild(pd.children, "year");
-      if (yearNode) {
-        const year = extractAllText(yearNode.children);
-        const monthNode = findChild(pd.children, "month");
-        const dayNode = findChild(pd.children, "day");
-        const date = { year };
-        if (monthNode) date.month = extractAllText(monthNode.children);
-        if (dayNode) date.day = extractAllText(dayNode.children);
-        publicationDate = date;
-      }
-    }
-  }
-  if (!publicationDate && pubDates.length > 0) {
-    const pd = pubDates[0];
-    const yearNode = findChild(pd.children, "year");
-    if (yearNode) {
-      const year = extractAllText(yearNode.children);
-      const monthNode = findChild(pd.children, "month");
-      const dayNode = findChild(pd.children, "day");
-      const date = { year };
-      if (monthNode) date.month = extractAllText(monthNode.children);
-      if (dayNode) date.day = extractAllText(dayNode.children);
-      publicationDate = date;
-    }
-  }
-  const articleType = article.attrs["article-type"] || void 0;
-  let license;
-  const permissions = findChild(metaChildren, "permissions");
-  if (permissions) {
-    const licenseNode = findChild(permissions.children, "license");
-    if (licenseNode) {
-      const href = licenseNode.attrs["xlink:href"];
-      if (href) {
-        license = href;
-      } else {
-        const licenseP = findChild(licenseNode.children, "license-p");
-        if (licenseP) license = extractAllText(licenseP.children).trim();
-      }
-    }
-  }
-  const kwdGroups = findChildren(metaChildren, "kwd-group");
-  const keywords = [];
-  for (const kwdGroup of kwdGroups) {
-    const kwds = findChildren(kwdGroup.children, "kwd");
-    for (const kwd of kwds) {
-      const text = extractAllText(kwd.children).trim();
-      if (text) keywords.push(text);
-    }
-  }
-  const volumeNode = findChild(metaChildren, "volume");
-  const volume = volumeNode ? extractAllText(volumeNode.children) : void 0;
-  const issueNode = findChild(metaChildren, "issue");
-  const issue = issueNode ? extractAllText(issueNode.children) : void 0;
-  let pages;
-  const fpageNode = findChild(metaChildren, "fpage");
-  const lpageNode = findChild(metaChildren, "lpage");
-  if (fpageNode) {
-    const fp = extractAllText(fpageNode.children);
-    const lp = lpageNode ? extractAllText(lpageNode.children) : "";
-    pages = lp ? `${fp}-${lp}` : fp;
-  } else {
-    const elocationNode = findChild(metaChildren, "elocation-id");
-    if (elocationNode) pages = extractAllText(elocationNode.children);
-  }
-  const journalMeta = findChild(front.children, "journal-meta");
-  let journal;
-  if (journalMeta) {
-    const titleGroup2 = findChild(journalMeta.children, "journal-title-group");
-    if (titleGroup2) {
-      const jTitle = findChild(titleGroup2.children, "journal-title");
-      if (jTitle) journal = extractAllText(jTitle.children);
-    }
-    if (!journal) {
-      const jTitle = findChild(journalMeta.children, "journal-title");
-      if (jTitle) journal = extractAllText(jTitle.children);
-    }
-  }
-  const result = { title, authors };
-  if (doi) result.doi = doi;
-  if (pmcid) result.pmcid = pmcid;
-  if (pmid) result.pmid = pmid;
-  if (journal) result.journal = journal;
-  if (publicationDate) result.publicationDate = publicationDate;
-  if (volume) result.volume = volume;
-  if (issue) result.issue = issue;
-  if (pages) result.pages = pages;
-  if (keywords.length > 0) result.keywords = keywords;
-  if (articleType) result.articleType = articleType;
-  if (license) result.license = license;
-  if (abstract) result.abstract = abstract;
-  return result;
-}
-function parseInlineContent(children) {
-  const result = [];
-  for (const child of children) {
-    const text = getTextContent(child);
-    if (text != null) {
-      if (text) result.push({ type: "text", text });
-      continue;
-    }
-    const tag = getTagName(child);
-    if (!tag) continue;
-    const innerChildren = getChildren(child);
-    if (tag === "bold") {
-      result.push({ type: "bold", children: parseInlineContent(innerChildren) });
-    } else if (tag === "italic") {
-      result.push({ type: "italic", children: parseInlineContent(innerChildren) });
-    } else if (tag === "sup") {
-      result.push({ type: "superscript", text: extractAllText(innerChildren) });
-    } else if (tag === "sub") {
-      result.push({ type: "subscript", text: extractAllText(innerChildren) });
-    } else if (tag === "inline-formula") {
-      let texMath = findChild(innerChildren, "tex-math");
-      if (!texMath) {
-        const alternatives = findChild(innerChildren, "alternatives");
-        if (alternatives) {
-          texMath = findChild(alternatives.children, "tex-math");
-        }
-      }
-      const tex = texMath ? extractAllText(texMath.children) : void 0;
-      const text2 = tex || extractAllText(innerChildren);
-      const entry = {
-        type: "inline-formula",
-        text: text2
-      };
-      if (tex) entry.tex = tex;
-      result.push(entry);
-    } else if (tag === "monospace") {
-      result.push({ type: "code", text: extractAllText(innerChildren) });
-    } else if (tag === "ext-link") {
-      const href = getAttr(child, "xlink:href");
-      if (href) {
-        result.push({ type: "link", url: href, children: parseInlineContent(innerChildren) });
-      } else {
-        const linkText = extractAllText(innerChildren);
-        if (linkText) result.push({ type: "text", text: linkText });
-      }
-    } else if (tag === "uri") {
-      const href = getAttr(child, "xlink:href");
-      const textContent = extractAllText(innerChildren);
-      const url = href || textContent;
-      if (url) {
-        result.push({ type: "link", url, children: parseInlineContent(innerChildren) });
-      }
-    } else if (tag === "underline" || tag === "sc") {
-      const passText = extractAllText(innerChildren);
-      if (passText) result.push({ type: "text", text: passText });
-    } else if (tag === "xref") {
-      const refType = getAttr(child, "ref-type");
-      if (refType === "bibr") {
-        result.push({
-          type: "citation",
-          refId: getAttr(child, "rid") ?? "",
-          text: extractAllText(innerChildren)
-        });
-      } else {
-        const xrefText = extractAllText(innerChildren);
-        if (xrefText) result.push({ type: "text", text: xrefText });
-      }
-    } else {
-      const unknownText = extractAllText(innerChildren);
-      if (unknownText) result.push({ type: "text", text: unknownText });
-    }
-  }
-  return result;
-}
-function parseList(listNode) {
-  const listType = getAttr(listNode, "list-type");
-  const ordered = listType === "order";
-  const listChildren = getChildren(listNode);
-  const listItems = findChildren(listChildren, "list-item");
-  const items = [];
-  for (const item of listItems) {
-    const pNodes = findChildren(item.children, "p");
-    const content = pNodes.flatMap((p) => parseInlineContent(p.children));
-    items.push(content);
-  }
-  return { type: "list", ordered, items };
-}
-function parseTableRow(trChildren) {
-  const cells = [];
-  for (const child of trChildren) {
-    const tag = getTagName(child);
-    if (tag === "th" || tag === "td") {
-      const cellChildren = getChildren(child);
-      const paragraphs = findChildren(cellChildren, "p");
-      if (paragraphs.length > 1) {
-        cells.push(
-          paragraphs.map((p) => extractAllText(p.children)).join("<br>")
-        );
-      } else {
-        cells.push(extractAllText(cellChildren));
-      }
-    }
-  }
-  return cells;
-}
-function parseTableWrap(tableWrapNode) {
-  const children = getChildren(tableWrapNode);
-  const labelNode = findChild(children, "label");
-  const label = labelNode ? extractAllText(labelNode.children) : "";
-  const captionNode = findChild(children, "caption");
-  const captionText = captionNode ? extractAllText(captionNode.children) : "";
-  const captionStr = [label, captionText].filter(Boolean).join(". ");
-  const tableNode = findChild(children, "table");
-  const result = {
-    headers: [],
-    rows: []
-  };
-  if (captionStr) result.caption = captionStr;
-  if (!tableNode) return result;
-  const thead = findChild(tableNode.children, "thead");
-  if (thead) {
-    const headRows = findChildren(thead.children, "tr");
-    if (headRows.length > 0) {
-      result.headers.push(...parseTableRow(headRows[0].children));
-    }
-  }
-  const tbody = findChild(tableNode.children, "tbody");
-  if (tbody) {
-    const bodyRows = findChildren(tbody.children, "tr");
-    for (const row of bodyRows) {
-      result.rows.push(parseTableRow(row.children));
-    }
-  }
-  return result;
-}
-function parseBoxedText(node) {
-  const children = getChildren(node);
-  const titleNode = findChild(children, "title");
-  const title = titleNode ? extractAllText(titleNode.children) : void 0;
-  const content = parseBlockContent(children);
-  const block = { type: "boxed-text", content };
-  if (title) block.title = title;
-  return block;
-}
-function parseDefList(node) {
-  const children = getChildren(node);
-  const titleNode = findChild(children, "title");
-  const title = titleNode ? extractAllText(titleNode.children) : void 0;
-  const defItems = findChildren(children, "def-item");
-  const items = [];
-  for (const item of defItems) {
-    const termNode = findChild(item.children, "term");
-    const defNode = findChild(item.children, "def");
-    const term = termNode ? extractAllText(termNode.children) : "";
-    const definition = defNode ? extractAllText(defNode.children) : "";
-    items.push({ term, definition });
-  }
-  const block = { type: "def-list", items };
-  if (title) block.title = title;
-  return block;
-}
-function parseDispFormula(node) {
-  const children = getChildren(node);
-  const id = getAttr(node, "id");
-  const labelNode = findChild(children, "label");
-  const label = labelNode ? extractAllText(labelNode.children) : void 0;
-  const alternatives = findChild(children, "alternatives");
-  const searchChildren = alternatives ? alternatives.children : children;
-  const texMath = findChild(searchChildren, "tex-math");
-  const block = { type: "formula" };
-  if (id) block.id = id;
-  if (label) block.label = label;
-  if (texMath) {
-    block.tex = extractAllText(texMath.children);
-  } else {
-    const textChildren = children.filter((c) => !("label" in c));
-    const text = extractAllText(textChildren).trim();
-    if (text) block.text = text;
-  }
-  return block;
-}
-const BLOCK_TAGS = /* @__PURE__ */ new Set(["table-wrap", "fig", "disp-quote", "boxed-text"]);
-function parseDispQuote(node) {
-  const children = getChildren(node);
-  const paragraphs = findChildren(children, "p");
-  const content = [];
-  for (let i = 0; i < paragraphs.length; i++) {
-    if (i > 0) content.push({ type: "text", text: "\n\n" });
-    const para = paragraphs[i];
-    if (para) content.push(...parseInlineContent(para.children));
-  }
-  if (paragraphs.length === 0) {
-    content.push(...parseInlineContent(children));
-  }
-  return { type: "blockquote", content };
-}
-function parseTableBlock(node) {
-  const tableResult = parseTableWrap(node);
-  const tableBlock = {
-    type: "table",
-    headers: tableResult.headers,
-    rows: tableResult.rows
-  };
-  if (tableResult.caption) tableBlock.caption = tableResult.caption;
-  return tableBlock;
-}
-function parseFigBlock(node) {
-  const innerChildren = getChildren(node);
-  const figBlock = { type: "figure" };
-  const figId = getAttr(node, "id");
-  if (figId) figBlock.id = figId;
-  const figLabel = findChild(innerChildren, "label");
-  if (figLabel) {
-    const labelText = extractAllText(figLabel.children);
-    if (labelText) figBlock.label = labelText;
-  }
-  const figCaption = findChild(innerChildren, "caption");
-  if (figCaption) {
-    const captionText = extractAllText(figCaption.children);
-    if (captionText) figBlock.caption = captionText;
-  }
-  return figBlock;
-}
-function parseParagraph(pChildren) {
-  const hasNestedBlocks = pChildren.some((child) => {
-    const tag = getTagName(child);
-    return tag != null && BLOCK_TAGS.has(tag);
-  });
-  if (!hasNestedBlocks) {
-    return [{ type: "paragraph", content: parseInlineContent(pChildren) }];
-  }
-  const blocks = [];
-  let inlineBuffer = [];
-  const flushInline = () => {
-    if (inlineBuffer.length > 0) {
-      const content = parseInlineContent(inlineBuffer);
-      const hasNonWhitespace = content.some(
-        (c) => c.type !== "text" || c.text.trim() !== ""
-      );
-      if (content.length > 0 && hasNonWhitespace) {
-        blocks.push({ type: "paragraph", content });
-      }
-      inlineBuffer = [];
-    }
-  };
-  for (const child of pChildren) {
-    const tag = getTagName(child);
-    if (tag === "table-wrap") {
-      flushInline();
-      blocks.push(parseTableBlock(child));
-    } else if (tag === "fig") {
-      flushInline();
-      blocks.push(parseFigBlock(child));
-    } else if (tag === "disp-quote") {
-      flushInline();
-      blocks.push(parseDispQuote(child));
-    } else if (tag === "boxed-text") {
-      flushInline();
-      blocks.push(parseBoxedText(child));
-    } else {
-      inlineBuffer.push(child);
-    }
-  }
-  flushInline();
-  return blocks;
-}
-function parseBlockContent(sectionChildren) {
-  const blocks = [];
-  for (const child of sectionChildren) {
-    const tag = getTagName(child);
-    if (!tag) continue;
-    if (tag === "p") {
-      blocks.push(...parseParagraph(getChildren(child)));
-    } else if (tag === "list") {
-      blocks.push(parseList(child));
-    } else if (tag === "table-wrap") {
-      blocks.push(parseTableBlock(child));
-    } else if (tag === "fig") {
-      blocks.push(parseFigBlock(child));
-    } else if (tag === "disp-quote") {
-      blocks.push(parseDispQuote(child));
-    } else if (tag === "boxed-text") {
-      blocks.push(parseBoxedText(child));
-    } else if (tag === "def-list") {
-      blocks.push(parseDefList(child));
-    } else if (tag === "disp-formula") {
-      blocks.push(parseDispFormula(child));
-    } else if (tag === "preformat") {
-      const text = extractAllText(getChildren(child));
-      blocks.push({ type: "preformat", text });
-    } else if (tag === "supplementary-material") {
-      const innerChildren = getChildren(child);
-      const labelNode = findChild(innerChildren, "label");
-      const captionNode = findChild(innerChildren, "caption");
-      const labelText = labelNode ? extractAllText(labelNode.children) : "";
-      const captionText = captionNode ? extractAllText(captionNode.children) : "";
-      const text = [labelText, captionText].filter(Boolean).join(": ");
-      if (text) {
-        blocks.push({ type: "paragraph", content: [{ type: "text", text }] });
-      }
-    }
-  }
-  return blocks;
-}
-function parseSection(secChildren, level) {
-  const titleNode = findChild(secChildren, "title");
-  const title = titleNode ? extractAllText(titleNode.children) : "";
-  const content = parseBlockContent(secChildren);
-  const subsections = [];
-  const nestedSecs = findChildren(secChildren, "sec");
-  for (const sub of nestedSecs) {
-    subsections.push(parseSection(sub.children, level + 1));
-  }
-  return { title, level, content, subsections };
-}
-function parseJatsBody(xml) {
-  const parsed = parser.parse(xml);
-  const article = findArticle(parsed);
-  if (!article) return [];
-  const body = findChild(article.children, "body");
-  if (!body) return [];
-  const sections = [];
-  const secs = findChildren(body.children, "sec");
-  if (secs.length > 0) {
-    for (const sec of secs) {
-      sections.push(parseSection(sec.children, 2));
-    }
-  } else {
-    const content = parseBlockContent(body.children);
-    if (content.length > 0) {
-      sections.push({ title: "", level: 2, content, subsections: [] });
-    }
-  }
-  return sections;
-}
-function formatElementCitation(children) {
-  const parts = [];
-  const personGroup = findChild(children, "person-group");
-  if (personGroup) {
-    const names = findChildren(personGroup.children, "name");
-    const authorParts = [];
-    for (const name of names) {
-      const surname = findChild(name.children, "surname");
-      const givenNames = findChild(name.children, "given-names");
-      const surnameText = surname ? extractAllText(surname.children) : "";
-      const givenText = givenNames ? extractAllText(givenNames.children) : "";
-      if (surnameText && givenText) {
-        authorParts.push(`${surnameText} ${givenText}`);
-      } else if (surnameText) {
-        authorParts.push(surnameText);
-      }
-    }
-    if (authorParts.length > 0) {
-      parts.push(authorParts.join(", "));
-    }
-  }
-  const articleTitle = findChild(children, "article-title");
-  if (articleTitle) {
-    parts.push(extractAllText(articleTitle.children));
-  }
-  const source = findChild(children, "source");
-  if (source) {
-    parts.push(extractAllText(source.children));
-  }
-  const year = findChild(children, "year");
-  const volume = findChild(children, "volume");
-  const fpage = findChild(children, "fpage");
-  const lpage = findChild(children, "lpage");
-  if (year) {
-    let yearStr = extractAllText(year.children);
-    if (volume) {
-      yearStr += `;${extractAllText(volume.children)}`;
-    }
-    if (fpage) {
-      const fpageText = extractAllText(fpage.children);
-      const lpageText = lpage ? extractAllText(lpage.children) : "";
-      yearStr += `:${fpageText}${lpageText ? `-${lpageText}` : ""}`;
-    }
-    parts.push(yearStr);
-  }
-  return parts.join(". ") + ".";
-}
-function extractMixedCitationText(children) {
-  const pubIds = findChildren(children, "pub-id");
-  const pubIdValues = pubIds.map((p) => extractAllText(p.children).trim()).filter(Boolean);
-  if (pubIdValues.length === 0) {
-    return extractAllText(children).trim();
-  }
-  const fullText = extractAllText(children).trim();
-  let result = fullText;
-  for (const val of pubIdValues) {
-    const escaped = val.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-    const matches = result.match(new RegExp(escaped, "g"));
-    if (matches && matches.length > 1) {
-      result = result.replace(val, "");
-      result = result.replace(/\s{2,}/g, " ").trim();
-    }
-  }
-  return result;
-}
-function extractPubIds(children) {
-  const pubIds = findChildren(children, "pub-id");
-  const result = {};
-  for (const p of pubIds) {
-    const idType = p.attrs["pub-id-type"];
-    const value = extractAllText(p.children).trim();
-    if (!value) continue;
-    if (idType === "doi") result.doi = value;
-    if (idType === "pmid") result.pmid = value;
-    if (idType === "pmc" || idType === "pmcid") {
-      result.pmcid = value.replace(/^PMC/, "");
-    }
-  }
-  return result;
-}
-function stripPubIdValues(text, pubIds) {
-  let result = text;
-  const values = [pubIds.doi, pubIds.pmid, pubIds.pmcid].filter(Boolean);
-  for (const val of values) {
-    const escaped = val.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-    result = result.replace(new RegExp(`(?:doi|PMID|pmid|PMC|pmc)[:\\s]*${escaped}`, "gi"), "");
-    result = result.replace(new RegExp(escaped, "g"), "");
-  }
-  if (pubIds.pmcid) {
-    const pmcFull = `PMC${pubIds.pmcid}`;
-    const escaped = pmcFull.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-    result = result.replace(new RegExp(`(?:pmc|pmcid)[:\\s]*${escaped}`, "gi"), "");
-    result = result.replace(new RegExp(escaped, "g"), "");
-  }
-  result = result.replace(/\s{2,}/g, " ").trim();
-  result = result.replace(/\.\s*\.$/, ".");
-  return result;
-}
-function parseJatsReferences(xml) {
-  const parsed = parser.parse(xml);
-  const article = findArticle(parsed);
-  if (!article) return [];
-  const back = findChild(article.children, "back");
-  if (!back) return [];
-  const refList = findChild(back.children, "ref-list");
-  if (!refList) return [];
-  const refs = findChildren(refList.children, "ref");
-  const references = [];
-  for (const ref of refs) {
-    const id = ref.attrs["id"] ?? "";
-    const citationAlternatives = findChild(ref.children, "citation-alternatives");
-    const searchChildren = citationAlternatives ? citationAlternatives.children : ref.children;
-    const mixedCitation = findChild(searchChildren, "mixed-citation");
-    if (mixedCitation) {
-      const rawText = extractMixedCitationText(mixedCitation.children);
-      const pubIds = extractPubIds(mixedCitation.children);
-      const text2 = stripPubIdValues(rawText, pubIds);
-      if (id && text2) references.push({ id, text: text2, ...pubIds });
-      continue;
-    }
-    const elementCitation = findChild(searchChildren, "element-citation");
-    if (elementCitation) {
-      const rawText = formatElementCitation(elementCitation.children);
-      const pubIds = extractPubIds(elementCitation.children);
-      const text2 = stripPubIdValues(rawText, pubIds);
-      if (id && text2) references.push({ id, text: text2, ...pubIds });
-      continue;
-    }
-    const childrenWithoutLabel = ref.children.filter((c) => !("label" in c));
-    const text = extractAllText(childrenWithoutLabel).trim();
-    if (id && text) {
-      references.push({ id, text });
-    }
-  }
-  return references;
-}
-function parseJatsBackMatter(xml) {
-  const parsed = parser.parse(xml);
-  const article = findArticle(parsed);
-  if (!article) return {};
-  const result = {};
-  const back = findChild(article.children, "back");
-  if (back) {
-    const ack = findChild(back.children, "ack");
-    if (ack) {
-      const paragraphs = findChildren(ack.children, "p");
-      if (paragraphs.length > 0) {
-        result.acknowledgments = paragraphs.map((p) => extractAllText(p.children)).join("\n\n");
-      }
-    }
-    const appGroup = findChild(back.children, "app-group");
-    if (appGroup) {
-      const apps = findChildren(appGroup.children, "app");
-      if (apps.length > 0) {
-        result.appendices = apps.map((app) => parseSection(app.children, 2));
-      }
-    }
-    const fnGroup = findChild(back.children, "fn-group");
-    if (fnGroup) {
-      const fns = findChildren(fnGroup.children, "fn");
-      if (fns.length > 0) {
-        result.footnotes = fns.map((fn) => {
-          const parts = [];
-          const titleNode = findChild(fn.children, "title");
-          if (titleNode) {
-            const titleText = extractAllText(titleNode.children).trim();
-            if (titleText) parts.push(titleText);
-          }
-          const paragraphs = findChildren(fn.children, "p");
-          for (const p of paragraphs) {
-            const pText = extractAllText(p.children).trim();
-            if (pText) parts.push(pText);
-          }
-          return {
-            id: fn.attrs["id"] ?? "",
-            text: parts.join(" ")
-          };
-        });
-      }
-    }
-    const notesElements = findChildren(back.children, "notes");
-    if (notesElements.length > 0) {
-      const notes = [];
-      for (const note of notesElements) {
-        const secs = findChildren(note.children, "sec");
-        const nestedNotes = findChildren(note.children, "notes");
-        const subItems = secs.length > 0 ? secs : nestedNotes;
-        if (subItems.length > 0) {
-          for (const sub of subItems) {
-            const subTitleNode = findChild(sub.children, "title");
-            const subTitle = subTitleNode ? extractAllText(subTitleNode.children) : "";
-            const subParagraphs = findChildren(sub.children, "p");
-            const subText = subParagraphs.map((p) => extractAllText(p.children)).join("\n\n");
-            if (subTitle || subText) {
-              notes.push({ title: subTitle, text: subText });
-            }
-          }
-        } else {
-          const titleNode = findChild(note.children, "title");
-          const title = titleNode ? extractAllText(titleNode.children) : "";
-          const paragraphs = findChildren(note.children, "p");
-          const text = paragraphs.map((p) => extractAllText(p.children)).join("\n\n");
-          if (title || text) {
-            notes.push({ title, text });
-          }
-        }
-      }
-      if (notes.length > 0) {
-        result.notes = notes;
-      }
-    }
-    const glossaryElements = findChildren(back.children, "glossary");
-    for (const glossary of glossaryElements) {
-      const titleNode = findChild(glossary.children, "title");
-      const title = titleNode ? extractAllText(titleNode.children) : "Glossary";
-      const defList = findChild(glossary.children, "def-list");
-      if (defList) {
-        const defItems = findChildren(defList.children, "def-item");
-        const lines = [];
-        for (const item of defItems) {
-          const termNode = findChild(item.children, "term");
-          const defNode = findChild(item.children, "def");
-          const term = termNode ? extractAllText(termNode.children) : "";
-          const definition = defNode ? extractAllText(defNode.children) : "";
-          lines.push(`${term}: ${definition}`);
-        }
-        if (!result.notes) result.notes = [];
-        result.notes.push({ title, text: lines.join("\n") });
-      }
-    }
-  }
-  const floatsGroup = findChild(article.children, "floats-group");
-  if (floatsGroup) {
-    const blocks = [];
-    for (const child of floatsGroup.children) {
-      const tag = getTagName(child);
-      if (tag === "fig") {
-        blocks.push(parseFigBlock(child));
-      } else if (tag === "table-wrap") {
-        blocks.push(parseTableBlock(child));
-      }
-    }
-    if (blocks.length > 0) {
-      result.floats = blocks;
-    }
-  }
-  return result;
-}
-export {
-  parseJatsBackMatter,
-  parseJatsBody,
-  parseJatsMetadata,
-  parseJatsReferences
-};
-//# sourceMappingURL=jats-parser.js.map