@ncukondo/search-hub 0.12.0 → 0.12.2

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

@@ -1 +0,0 @@
-{"version":3,"file":"jats-parser.js","sources":["../../../src/fulltext/convert/jats-parser.ts"],"sourcesContent":["/**\n * JATS XML parser for PMC articles.\n *\n * Parses JATS (Journal Article Tag Suite) XML into an intermediate\n * representation for Markdown conversion.\n *\n * Uses fast-xml-parser with `preserveOrder: true` to maintain document order\n * of interleaved elements (e.g. text, citations, formatting).\n */\n\nimport { XMLParser } from 'fast-xml-parser';\nimport type {\n  JatsAuthor,\n  JatsMetadata,\n  JatsSection,\n  JatsReference,\n  JatsFootnote,\n  BackMatterNote,\n  BlockElement,\n  InlineContent,\n} from './types.js';\n\n/**\n * A node in the preserveOrder output.\n * Either a text node `{ \"#text\": string | number }` or an element node\n * `{ tagName: OrderedNode[], \":@\"?: { \"@_attr\": value } }`.\n */\ntype OrderedNode = Record<string, unknown>;\n\nconst parser = new XMLParser({\n  ignoreAttributes: false,\n  attributeNamePrefix: '@_',\n  textNodeName: '#text',\n  trimValues: false,\n  preserveOrder: true,\n  processEntities: true,\n  htmlEntities: true,\n});\n\n// ─── Navigation Helpers ──────────────────────────────────────────────\n\n/** Get the tag name of an ordered node (the first key that isn't \":@\" or \"#text\"). */\nfunction getTagName(node: OrderedNode): string | undefined {\n  for (const key of Object.keys(node)) {\n    if (key !== ':@' && key !== '#text') return key;\n  }\n  return undefined;\n}\n\n/** Get the children array of an element node. */\nfunction getChildren(node: OrderedNode): OrderedNode[] {\n  const tag = getTagName(node);\n  if (!tag) return [];\n  const children = node[tag];\n  return Array.isArray(children) ? (children as OrderedNode[]) : [];\n}\n\n/** Get attributes of an element node. */\nfunction getAttr(node: OrderedNode, attrName: string): string | undefined {\n  const attrs = node[':@'] as Record<string, unknown> | undefined;\n  if (!attrs) return undefined;\n  const val = attrs[`@_${attrName}`];\n  return val != null ? String(val) : undefined;\n}\n\n/** Get all attributes of an element node (strips @_ prefix for consistency with getAttr). */\nfunction getAttrs(node: OrderedNode): Record<string, string> {\n  const attrs = node[':@'] as Record<string, unknown> | undefined;\n  if (!attrs) return {};\n  const result: Record<string, string> = {};\n  for (const [key, value] of Object.entries(attrs)) {\n    if (key.startsWith('@_')) {\n      result[key.slice(2)] = String(value);\n    }\n  }\n  return result;\n}\n\n/** Find the first child element with the given tag name. */\nfunction findChild(\n  children: OrderedNode[],\n  tagName: string,\n): { node: OrderedNode; children: OrderedNode[]; attrs: Record<string, string> } | undefined {\n  for (const child of children) {\n    if (tagName in child) {\n      const childArr = child[tagName];\n      return {\n        node: child,\n        children: Array.isArray(childArr) ? (childArr as OrderedNode[]) : [],\n        attrs: getAttrs(child),\n      };\n    }\n  }\n  return undefined;\n}\n\n/** Find all child elements with the given tag name. */\nfunction findChildren(\n  children: OrderedNode[],\n  tagName: string,\n): Array<{ node: OrderedNode; children: OrderedNode[]; attrs: Record<string, string> }> {\n  const results: Array<{\n    node: OrderedNode;\n    children: OrderedNode[];\n    attrs: Record<string, string>;\n  }> = [];\n  for (const child of children) {\n    if (tagName in child) {\n      const childArr = child[tagName];\n      results.push({\n        node: child,\n        children: Array.isArray(childArr) ? (childArr as OrderedNode[]) : [],\n        attrs: getAttrs(child),\n      });\n    }\n  }\n  return results;\n}\n\n/** Get text content from a #text node. */\nfunction getTextContent(child: OrderedNode): string | undefined {\n  if ('#text' in child) {\n    const val = child['#text'];\n    return val != null ? String(val) : undefined;\n  }\n  return undefined;\n}\n\n/**\n * Find the <article> element, handling optional <pmc-articleset> wrapper\n * that appears in efetch responses.\n */\nfunction findArticle(\n  parsed: OrderedNode[],\n): { node: OrderedNode; children: OrderedNode[]; attrs: Record<string, string> } | undefined {\n  const direct = findChild(parsed, 'article');\n  if (direct) return direct;\n  const wrapper = findChild(parsed, 'pmc-articleset');\n  if (wrapper) return findChild(wrapper.children, 'article');\n  return undefined;\n}\n\n// ─── Text Extraction ─────────────────────────────────────────────────\n\n/** Tags whose text content should be followed by a space when adjacent to other content. */\nconst SPACE_AFTER_TAGS = new Set([\n  'surname',\n  'given-names',\n  'name',\n  'string-name',\n]);\n\n/**\n * Extract plain text from a node that may contain nested elements.\n * Recursively collects all text content from preserveOrder nodes.\n *\n * When extracting text from inline container elements (e.g. `<name>`,\n * `<string-name>`), inserts a space between adjacent child elements\n * that would otherwise concatenate without whitespace (e.g.\n * `<surname>McGuire</surname><given-names>N</given-names>` → `McGuire N`).\n */\nfunction extractAllText(node: unknown): string {\n  if (node == null) return '';\n  if (typeof node === 'string') return node;\n  if (typeof node === 'number') return String(node);\n  if (Array.isArray(node)) {\n    return joinChildTexts(node);\n  }\n  if (typeof node === 'object') {\n    const obj = node as OrderedNode;\n    // Text node\n    const text = getTextContent(obj);\n    if (text != null) return text;\n    // Element node — recurse into children\n    const tag = getTagName(obj);\n    if (tag) {\n      const children = obj[tag];\n      if (Array.isArray(children)) {\n        return joinChildTexts(children as OrderedNode[]);\n      }\n    }\n  }\n  return '';\n}\n\n/**\n * Join extracted text from an array of child nodes, inserting spaces\n * between adjacent inline elements where no whitespace separator exists.\n */\nfunction joinChildTexts(children: OrderedNode[]): string {\n  const parts: string[] = [];\n  for (const child of children) {\n    const text = extractAllText(child);\n    if (!text) continue;\n\n    const tag = getTagName(child as OrderedNode);\n\n    // If this is a space-after tag and there's previous content that doesn't\n    // end with whitespace or punctuation, insert a space before this text.\n    if (tag && SPACE_AFTER_TAGS.has(tag) && parts.length > 0) {\n      const prev = parts[parts.length - 1]!;\n      if (prev && !/[\\s,;.:()\\-/]$/.test(prev)) {\n        parts.push(' ');\n      }\n    }\n\n    parts.push(text);\n\n    // If this is a space-after tag, check if a space is needed after.\n    // We handle this by peeking: space will be inserted before the next\n    // element if needed (handled above). But we also need to handle\n    // the case where the next sibling is a text node starting without space.\n    // That's already handled since text nodes include their own whitespace.\n  }\n  return parts.join('');\n}\n\n// ─── Metadata Parsing ────────────────────────────────────────────────\n\n/**\n * Parse JATS XML front matter to extract article metadata.\n */\nexport function parseJatsMetadata(xml: string): JatsMetadata {\n  const parsed = parser.parse(xml) as OrderedNode[];\n  const article = findArticle(parsed);\n  if (!article) return { title: '', authors: [] };\n\n  const front = findChild(article.children, 'front');\n  if (!front) return { title: '', authors: [] };\n\n  const articleMeta = findChild(front.children, 'article-meta');\n  if (!articleMeta) return { title: '', authors: [] };\n\n  const metaChildren = articleMeta.children;\n\n  // Title\n  const titleGroup = findChild(metaChildren, 'title-group');\n  const articleTitle = titleGroup ? findChild(titleGroup.children, 'article-title') : undefined;\n  const title = articleTitle ? extractAllText(articleTitle.children) : '';\n\n  // Article IDs\n  const articleIds = findChildren(metaChildren, 'article-id');\n  let doi: string | undefined;\n  let pmcid: string | undefined;\n  let pmid: string | undefined;\n  for (const idEntry of articleIds) {\n    const idType = idEntry.attrs['pub-id-type'];\n    const idText = extractAllText(idEntry.children);\n    if (idType === 'doi') doi = idText;\n    if (idType === 'pmc' || idType === 'pmcid') {\n      pmcid = idText.replace(/^PMC/, '');\n    }\n    if (idType === 'pmid') pmid = idText;\n  }\n\n  // Authors\n  const authors: JatsAuthor[] = [];\n  const contribGroup = findChild(metaChildren, 'contrib-group');\n  if (contribGroup) {\n    const contribs = findChildren(contribGroup.children, 'contrib');\n    for (const contrib of contribs) {\n      if (contrib.attrs['contrib-type'] !== 'author') continue;\n      const nameNode = findChild(contrib.children, 'name');\n      if (!nameNode) continue;\n      const surnameNode = findChild(nameNode.children, 'surname');\n      const givenNamesNode = findChild(nameNode.children, 'given-names');\n      const author: JatsAuthor = {\n        surname: surnameNode ? extractAllText(surnameNode.children) : '',\n      };\n      const givenNames = givenNamesNode ? extractAllText(givenNamesNode.children) : '';\n      if (givenNames) {\n        author.givenNames = givenNames;\n      }\n      authors.push(author);\n    }\n  }\n\n  // Abstract\n  const abstractNode = findChild(metaChildren, 'abstract');\n  let abstract: string | undefined;\n  if (abstractNode) {\n    // Structured abstract with <sec> elements\n    const sections = findChildren(abstractNode.children, 'sec');\n    if (sections.length > 0) {\n      const parts: string[] = [];\n      for (const sec of sections) {\n        const secTitleNode = findChild(sec.children, 'title');\n        const secTitle = secTitleNode ? extractAllText(secTitleNode.children) : '';\n        const secPs = findChildren(sec.children, 'p');\n        const text = secPs.map((p) => extractAllText(p.children)).join(' ');\n        if (secTitle) {\n          parts.push(`${secTitle}: ${text}`);\n        } else {\n          parts.push(text);\n        }\n      }\n      abstract = parts.join('\\n\\n');\n    } else {\n      // Simple abstract with <p>\n      const paragraphs = findChildren(abstractNode.children, 'p');\n      if (paragraphs.length > 0) {\n        abstract = paragraphs.map((p) => extractAllText(p.children)).join('\\n\\n');\n      } else {\n        const text = extractAllText(abstractNode.children);\n        if (text) abstract = text;\n      }\n    }\n  }\n\n  // Publication date (from <article-meta>/<pub-date>)\n  // Priority: epub > ppub > collection > any other\n  const pubDates = findChildren(metaChildren, 'pub-date');\n  let publicationDate: { year: string; month?: string; day?: string } | undefined;\n  const datePriority: Record<string, number> = { epub: 0, ppub: 1, collection: 2 };\n  let bestPriority = Infinity;\n  for (const pd of pubDates) {\n    // Support both pub-type (NLM/early JATS) and date-type (JATS 1.2+)\n    const dateType = pd.attrs['pub-type'] ?? pd.attrs['date-type'] ?? '';\n    const priority = datePriority[dateType] ?? 3;\n    if (priority < bestPriority) {\n      bestPriority = priority;\n      const yearNode = findChild(pd.children, 'year');\n      if (yearNode) {\n        const year = extractAllText(yearNode.children);\n        const monthNode = findChild(pd.children, 'month');\n        const dayNode = findChild(pd.children, 'day');\n        const date: { year: string; month?: string; day?: string } = { year };\n        if (monthNode) date.month = extractAllText(monthNode.children);\n        if (dayNode) date.day = extractAllText(dayNode.children);\n        publicationDate = date;\n      }\n    }\n  }\n  // If no prioritized date found, take first available\n  if (!publicationDate && pubDates.length > 0) {\n    const pd = pubDates[0]!;\n    const yearNode = findChild(pd.children, 'year');\n    if (yearNode) {\n      const year = extractAllText(yearNode.children);\n      const monthNode = findChild(pd.children, 'month');\n      const dayNode = findChild(pd.children, 'day');\n      const date: { year: string; month?: string; day?: string } = { year };\n      if (monthNode) date.month = extractAllText(monthNode.children);\n      if (dayNode) date.day = extractAllText(dayNode.children);\n      publicationDate = date;\n    }\n  }\n\n  // Article type (from root <article> element attribute)\n  const articleType = article.attrs['article-type'] || undefined;\n\n  // License (from <permissions>/<license>)\n  let license: string | undefined;\n  const permissions = findChild(metaChildren, 'permissions');\n  if (permissions) {\n    const licenseNode = findChild(permissions.children, 'license');\n    if (licenseNode) {\n      // Prefer @xlink:href (standardized URL) over <license-p> (free-text)\n      const href = licenseNode.attrs['xlink:href'];\n      if (href) {\n        license = href;\n      } else {\n        const licenseP = findChild(licenseNode.children, 'license-p');\n        if (licenseP) license = extractAllText(licenseP.children).trim();\n      }\n    }\n  }\n\n  // Keywords (from all <kwd-group> elements)\n  const kwdGroups = findChildren(metaChildren, 'kwd-group');\n  const keywords: string[] = [];\n  for (const kwdGroup of kwdGroups) {\n    const kwds = findChildren(kwdGroup.children, 'kwd');\n    for (const kwd of kwds) {\n      const text = extractAllText(kwd.children).trim();\n      if (text) keywords.push(text);\n    }\n  }\n\n  // Volume, issue, pages\n  const volumeNode = findChild(metaChildren, 'volume');\n  const volume = volumeNode ? extractAllText(volumeNode.children) : undefined;\n  const issueNode = findChild(metaChildren, 'issue');\n  const issue = issueNode ? extractAllText(issueNode.children) : undefined;\n  let pages: string | undefined;\n  const fpageNode = findChild(metaChildren, 'fpage');\n  const lpageNode = findChild(metaChildren, 'lpage');\n  if (fpageNode) {\n    const fp = extractAllText(fpageNode.children);\n    const lp = lpageNode ? extractAllText(lpageNode.children) : '';\n    pages = lp ? `${fp}-${lp}` : fp;\n  } else {\n    const elocationNode = findChild(metaChildren, 'elocation-id');\n    if (elocationNode) pages = extractAllText(elocationNode.children);\n  }\n\n  // Journal name (from <front>/<journal-meta>)\n  const journalMeta = findChild(front.children, 'journal-meta');\n  let journal: string | undefined;\n  if (journalMeta) {\n    const titleGroup = findChild(journalMeta.children, 'journal-title-group');\n    if (titleGroup) {\n      const jTitle = findChild(titleGroup.children, 'journal-title');\n      if (jTitle) journal = extractAllText(jTitle.children);\n    }\n    if (!journal) {\n      const jTitle = findChild(journalMeta.children, 'journal-title');\n      if (jTitle) journal = extractAllText(jTitle.children);\n    }\n  }\n\n  const result: JatsMetadata = { title, authors };\n  if (doi) result.doi = doi;\n  if (pmcid) result.pmcid = pmcid;\n  if (pmid) result.pmid = pmid;\n  if (journal) result.journal = journal;\n  if (publicationDate) result.publicationDate = publicationDate;\n  if (volume) result.volume = volume;\n  if (issue) result.issue = issue;\n  if (pages) result.pages = pages;\n  if (keywords.length > 0) result.keywords = keywords;\n  if (articleType) result.articleType = articleType;\n  if (license) result.license = license;\n  if (abstract) result.abstract = abstract;\n  return result;\n}\n\n// ─── Inline Content Parsing ──────────────────────────────────────────\n\n/**\n * Parse inline content from a paragraph's children array.\n * Iterates in document order to preserve interleaving of text, citations,\n * and formatting elements.\n */\nfunction parseInlineContent(children: OrderedNode[]): InlineContent[] {\n  const result: InlineContent[] = [];\n\n  for (const child of children) {\n    // Text node\n    const text = getTextContent(child);\n    if (text != null) {\n      if (text) result.push({ type: 'text', text });\n      continue;\n    }\n\n    const tag = getTagName(child);\n    if (!tag) continue;\n\n    const innerChildren = getChildren(child);\n\n    if (tag === 'bold') {\n      result.push({ type: 'bold', children: parseInlineContent(innerChildren) });\n    } else if (tag === 'italic') {\n      result.push({ type: 'italic', children: parseInlineContent(innerChildren) });\n    } else if (tag === 'sup') {\n      result.push({ type: 'superscript', text: extractAllText(innerChildren) });\n    } else if (tag === 'sub') {\n      result.push({ type: 'subscript', text: extractAllText(innerChildren) });\n    } else if (tag === 'inline-formula') {\n      // Try to find <tex-math> directly or inside <alternatives>\n      let texMath = findChild(innerChildren, 'tex-math');\n      if (!texMath) {\n        const alternatives = findChild(innerChildren, 'alternatives');\n        if (alternatives) {\n          texMath = findChild(alternatives.children, 'tex-math');\n        }\n      }\n      const tex = texMath ? extractAllText(texMath.children) : undefined;\n      const text = tex || extractAllText(innerChildren);\n      const entry: { type: 'inline-formula'; tex?: string; text: string } = {\n        type: 'inline-formula',\n        text,\n      };\n      if (tex) entry.tex = tex;\n      result.push(entry);\n    } else if (tag === 'monospace') {\n      result.push({ type: 'code', text: extractAllText(innerChildren) });\n    } else if (tag === 'ext-link') {\n      const href = getAttr(child, 'xlink:href');\n      if (href) {\n        result.push({ type: 'link', url: href, children: parseInlineContent(innerChildren) });\n      } else {\n        const linkText = extractAllText(innerChildren);\n        if (linkText) result.push({ type: 'text', text: linkText });\n      }\n    } else if (tag === 'uri') {\n      const href = getAttr(child, 'xlink:href');\n      const textContent = extractAllText(innerChildren);\n      const url = href || textContent;\n      if (url) {\n        result.push({ type: 'link', url, children: parseInlineContent(innerChildren) });\n      }\n    } else if (tag === 'underline' || tag === 'sc') {\n      // Pass-through: preserve text content without special formatting\n      const passText = extractAllText(innerChildren);\n      if (passText) result.push({ type: 'text', text: passText });\n    } else if (tag === 'xref') {\n      const refType = getAttr(child, 'ref-type');\n      if (refType === 'bibr') {\n        result.push({\n          type: 'citation',\n          refId: getAttr(child, 'rid') ?? '',\n          text: extractAllText(innerChildren),\n        });\n      } else {\n        const xrefText = extractAllText(innerChildren);\n        if (xrefText) result.push({ type: 'text', text: xrefText });\n      }\n    } else {\n      // Unknown inline element — extract text\n      const unknownText = extractAllText(innerChildren);\n      if (unknownText) result.push({ type: 'text', text: unknownText });\n    }\n  }\n\n  return result;\n}\n\n// ─── Block Content Parsing ───────────────────────────────────────────\n\n/**\n * Parse a <list> element into a BlockElement.\n */\nfunction parseList(listNode: OrderedNode): BlockElement {\n  const listType = getAttr(listNode, 'list-type');\n  const ordered = listType === 'order';\n  const listChildren = getChildren(listNode);\n  const listItems = findChildren(listChildren, 'list-item');\n  const items: InlineContent[][] = [];\n\n  for (const item of listItems) {\n    const pNodes = findChildren(item.children, 'p');\n    const content = pNodes.flatMap((p) => parseInlineContent(p.children));\n    items.push(content);\n  }\n\n  return { type: 'list', ordered, items };\n}\n\n/**\n * Parse a table row into an array of cell text content.\n */\nfunction parseTableRow(trChildren: OrderedNode[]): string[] {\n  const cells: string[] = [];\n  for (const child of trChildren) {\n    const tag = getTagName(child);\n    if (tag === 'th' || tag === 'td') {\n      const cellChildren = getChildren(child);\n      // Check if cell contains multiple <p> elements\n      const paragraphs = findChildren(cellChildren, 'p');\n      if (paragraphs.length > 1) {\n        cells.push(\n          paragraphs.map((p) => extractAllText(p.children)).join('<br>'),\n        );\n      } else {\n        cells.push(extractAllText(cellChildren));\n      }\n    }\n  }\n  return cells;\n}\n\n/**\n * Parse an already-parsed table-wrap node.\n */\nfunction parseTableWrap(tableWrapNode: OrderedNode): {\n  caption?: string;\n  headers: string[];\n  rows: string[][];\n} {\n  const children = getChildren(tableWrapNode);\n\n  // Caption\n  const labelNode = findChild(children, 'label');\n  const label = labelNode ? extractAllText(labelNode.children) : '';\n  const captionNode = findChild(children, 'caption');\n  const captionText = captionNode ? extractAllText(captionNode.children) : '';\n  const captionStr = [label, captionText].filter(Boolean).join('. ');\n\n  const tableNode = findChild(children, 'table');\n  const result: { caption?: string; headers: string[]; rows: string[][] } = {\n    headers: [],\n    rows: [],\n  };\n  if (captionStr) result.caption = captionStr;\n  if (!tableNode) return result;\n\n  // Headers from thead\n  const thead = findChild(tableNode.children, 'thead');\n  if (thead) {\n    const headRows = findChildren(thead.children, 'tr');\n    if (headRows.length > 0) {\n      result.headers.push(...parseTableRow(headRows[0]!.children));\n    }\n  }\n\n  // Body rows\n  const tbody = findChild(tableNode.children, 'tbody');\n  if (tbody) {\n    const bodyRows = findChildren(tbody.children, 'tr');\n    for (const row of bodyRows) {\n      result.rows.push(parseTableRow(row.children));\n    }\n  }\n\n  return result;\n}\n\n/**\n * Parse a <table-wrap> element into a table block.\n * Exported for standalone use and used internally by parseBlockContent.\n */\nexport function parseJatsTable(xml: string): {\n  caption?: string;\n  headers: string[];\n  rows: string[][];\n} {\n  const parsed = parser.parse(xml) as OrderedNode[];\n  const tableWrap = findChild(parsed, 'table-wrap');\n  if (tableWrap) {\n    return parseTableWrap(tableWrap.node);\n  }\n  // Fallback: if not wrapped, try to find table directly\n  return { headers: [], rows: [] };\n}\n\n/**\n * Parse a <boxed-text> element into a boxed-text block.\n * Extracts optional title and recursively parses inner block content.\n */\nfunction parseBoxedText(node: OrderedNode): BlockElement {\n  const children = getChildren(node);\n  const titleNode = findChild(children, 'title');\n  const title = titleNode ? extractAllText(titleNode.children) : undefined;\n  const content = parseBlockContent(children);\n  const block: BlockElement = { type: 'boxed-text', content };\n  if (title) block.title = title;\n  return block;\n}\n\n/**\n * Parse a <def-list> element into a def-list block.\n * Extracts optional title and <def-item> pairs with <term> and <def>.\n */\nfunction parseDefList(node: OrderedNode): BlockElement {\n  const children = getChildren(node);\n  const titleNode = findChild(children, 'title');\n  const title = titleNode ? extractAllText(titleNode.children) : undefined;\n  const defItems = findChildren(children, 'def-item');\n  const items: { term: string; definition: string }[] = [];\n  for (const item of defItems) {\n    const termNode = findChild(item.children, 'term');\n    const defNode = findChild(item.children, 'def');\n    const term = termNode ? extractAllText(termNode.children) : '';\n    const definition = defNode ? extractAllText(defNode.children) : '';\n    items.push({ term, definition });\n  }\n  const block: BlockElement = { type: 'def-list', items };\n  if (title) block.title = title;\n  return block;\n}\n\n/**\n * Parse a <disp-formula> element into a formula block.\n * Extracts TeX content from <tex-math> preferentially (inside <alternatives> or direct),\n * falls back to extractAllText for plain text.\n */\nfunction parseDispFormula(node: OrderedNode): BlockElement {\n  const children = getChildren(node);\n  const id = getAttr(node, 'id');\n  const labelNode = findChild(children, 'label');\n  const label = labelNode ? extractAllText(labelNode.children) : undefined;\n\n  // Try <alternatives> wrapper first\n  const alternatives = findChild(children, 'alternatives');\n  const searchChildren = alternatives ? alternatives.children : children;\n\n  const texMath = findChild(searchChildren, 'tex-math');\n  const block: BlockElement = { type: 'formula' };\n  if (id) block.id = id;\n  if (label) block.label = label;\n\n  if (texMath) {\n    block.tex = extractAllText(texMath.children);\n  } else {\n    // Fall back to plain text extraction (skip label)\n    const textChildren = children.filter((c) => !('label' in c));\n    const text = extractAllText(textChildren).trim();\n    if (text) block.text = text;\n  }\n\n  return block;\n}\n\n/** Tags that represent block-level elements when nested inside <p>. */\nconst BLOCK_TAGS = new Set(['table-wrap', 'fig', 'disp-quote', 'boxed-text']);\n\n/**\n * Parse a <disp-quote> element into a blockquote block.\n * Extracts <p> children and concatenates their inline content.\n */\nfunction parseDispQuote(node: OrderedNode): BlockElement {\n  const children = getChildren(node);\n  const paragraphs = findChildren(children, 'p');\n  const content: InlineContent[] = [];\n  for (let i = 0; i < paragraphs.length; i++) {\n    if (i > 0) content.push({ type: 'text', text: '\\n\\n' });\n    const para = paragraphs[i];\n    if (para) content.push(...parseInlineContent(para.children));\n  }\n  // If no <p> children, extract inline content directly\n  if (paragraphs.length === 0) {\n    content.push(...parseInlineContent(children));\n  }\n  return { type: 'blockquote', content };\n}\n\n/**\n * Parse a <table-wrap> node into a table block element.\n */\nfunction parseTableBlock(node: OrderedNode): BlockElement {\n  const tableResult = parseTableWrap(node);\n  const tableBlock: BlockElement = {\n    type: 'table',\n    headers: tableResult.headers,\n    rows: tableResult.rows,\n  };\n  if (tableResult.caption) tableBlock.caption = tableResult.caption;\n  return tableBlock;\n}\n\n/**\n * Parse a <fig> node into a figure block element.\n */\nfunction parseFigBlock(node: OrderedNode): BlockElement {\n  const innerChildren = getChildren(node);\n  const figBlock: BlockElement = { type: 'figure' };\n  const figId = getAttr(node, 'id');\n  if (figId) figBlock.id = figId;\n  const figLabel = findChild(innerChildren, 'label');\n  if (figLabel) {\n    const labelText = extractAllText(figLabel.children);\n    if (labelText) figBlock.label = labelText;\n  }\n  const figCaption = findChild(innerChildren, 'caption');\n  if (figCaption) {\n    const captionText = extractAllText(figCaption.children);\n    if (captionText) figBlock.caption = captionText;\n  }\n  return figBlock;\n}\n\n/**\n * Parse a <p> element, splitting it if it contains nested block elements\n * (table-wrap, fig, disp-quote). Returns one or more block elements.\n */\nfunction parseParagraph(pChildren: OrderedNode[]): BlockElement[] {\n  // Check if <p> contains any nested block elements\n  const hasNestedBlocks = pChildren.some((child) => {\n    const tag = getTagName(child);\n    return tag != null && BLOCK_TAGS.has(tag);\n  });\n\n  if (!hasNestedBlocks) {\n    return [{ type: 'paragraph', content: parseInlineContent(pChildren) }];\n  }\n\n  // Split into inline runs and block elements\n  const blocks: BlockElement[] = [];\n  let inlineBuffer: OrderedNode[] = [];\n\n  const flushInline = () => {\n    if (inlineBuffer.length > 0) {\n      const content = parseInlineContent(inlineBuffer);\n      // Skip whitespace-only paragraphs created by XML formatting\n      const hasNonWhitespace = content.some(\n        (c) => c.type !== 'text' || c.text.trim() !== '',\n      );\n      if (content.length > 0 && hasNonWhitespace) {\n        blocks.push({ type: 'paragraph', content });\n      }\n      inlineBuffer = [];\n    }\n  };\n\n  for (const child of pChildren) {\n    const tag = getTagName(child);\n    if (tag === 'table-wrap') {\n      flushInline();\n      blocks.push(parseTableBlock(child));\n    } else if (tag === 'fig') {\n      flushInline();\n      blocks.push(parseFigBlock(child));\n    } else if (tag === 'disp-quote') {\n      flushInline();\n      blocks.push(parseDispQuote(child));\n    } else if (tag === 'boxed-text') {\n      flushInline();\n      blocks.push(parseBoxedText(child));\n    } else {\n      inlineBuffer.push(child);\n    }\n  }\n  flushInline();\n\n  return blocks;\n}\n\n/**\n * Parse block-level content from a section's children.\n * Iterates in document order to preserve ordering of paragraphs, lists,\n * tables, figures, and blockquotes.\n */\nfunction parseBlockContent(sectionChildren: OrderedNode[]): BlockElement[] {\n  const blocks: BlockElement[] = [];\n\n  for (const child of sectionChildren) {\n    const tag = getTagName(child);\n    if (!tag) continue;\n\n    if (tag === 'p') {\n      blocks.push(...parseParagraph(getChildren(child)));\n    } else if (tag === 'list') {\n      blocks.push(parseList(child));\n    } else if (tag === 'table-wrap') {\n      blocks.push(parseTableBlock(child));\n    } else if (tag === 'fig') {\n      blocks.push(parseFigBlock(child));\n    } else if (tag === 'disp-quote') {\n      blocks.push(parseDispQuote(child));\n    } else if (tag === 'boxed-text') {\n      blocks.push(parseBoxedText(child));\n    } else if (tag === 'def-list') {\n      blocks.push(parseDefList(child));\n    } else if (tag === 'disp-formula') {\n      blocks.push(parseDispFormula(child));\n    } else if (tag === 'preformat') {\n      const text = extractAllText(getChildren(child));\n      blocks.push({ type: 'preformat', text });\n    } else if (tag === 'supplementary-material') {\n      const innerChildren = getChildren(child);\n      const labelNode = findChild(innerChildren, 'label');\n      const captionNode = findChild(innerChildren, 'caption');\n      const labelText = labelNode ? extractAllText(labelNode.children) : '';\n      const captionText = captionNode ? extractAllText(captionNode.children) : '';\n      const text = [labelText, captionText].filter(Boolean).join(': ');\n      if (text) {\n        blocks.push({ type: 'paragraph', content: [{ type: 'text', text }] });\n      }\n    }\n    // Skip title, sec, and other non-block elements\n  }\n\n  return blocks;\n}\n\n// ─── Section Parsing ─────────────────────────────────────────────────\n\n/**\n * Parse a <sec> element into a JatsSection, recursively handling subsections.\n */\nfunction parseSection(secChildren: OrderedNode[], level: number): JatsSection {\n  const titleNode = findChild(secChildren, 'title');\n  const title = titleNode ? extractAllText(titleNode.children) : '';\n  const content = parseBlockContent(secChildren);\n\n  // Nested sections\n  const subsections: JatsSection[] = [];\n  const nestedSecs = findChildren(secChildren, 'sec');\n  for (const sub of nestedSecs) {\n    subsections.push(parseSection(sub.children, level + 1));\n  }\n\n  return { title, level, content, subsections };\n}\n\n/**\n * Parse JATS XML body to extract sections and content.\n */\nexport function parseJatsBody(xml: string): JatsSection[] {\n  const parsed = parser.parse(xml) as OrderedNode[];\n  const article = findArticle(parsed);\n  if (!article) return [];\n\n  const body = findChild(article.children, 'body');\n  if (!body) return [];\n\n  const sections: JatsSection[] = [];\n  const secs = findChildren(body.children, 'sec');\n\n  if (secs.length > 0) {\n    for (const sec of secs) {\n      sections.push(parseSection(sec.children, 2));\n    }\n  } else {\n    // Body has paragraphs without sections\n    const content = parseBlockContent(body.children);\n    if (content.length > 0) {\n      sections.push({ title: '', level: 2, content, subsections: [] });\n    }\n  }\n\n  return sections;\n}\n\n// ─── Reference Parsing ───────────────────────────────────────────────\n\n/**\n * Format a structured <element-citation> into a readable reference string.\n * Produces: \"Author1, Author2. Title. Source. Year;Volume:FirstPage-LastPage.\"\n */\nfunction formatElementCitation(children: OrderedNode[]): string {\n  const parts: string[] = [];\n\n  // Authors from person-group\n  const personGroup = findChild(children, 'person-group');\n  if (personGroup) {\n    const names = findChildren(personGroup.children, 'name');\n    const authorParts: string[] = [];\n    for (const name of names) {\n      const surname = findChild(name.children, 'surname');\n      const givenNames = findChild(name.children, 'given-names');\n      const surnameText = surname ? extractAllText(surname.children) : '';\n      const givenText = givenNames ? extractAllText(givenNames.children) : '';\n      if (surnameText && givenText) {\n        authorParts.push(`${surnameText} ${givenText}`);\n      } else if (surnameText) {\n        authorParts.push(surnameText);\n      }\n    }\n    if (authorParts.length > 0) {\n      parts.push(authorParts.join(', '));\n    }\n  }\n\n  // Article title\n  const articleTitle = findChild(children, 'article-title');\n  if (articleTitle) {\n    parts.push(extractAllText(articleTitle.children));\n  }\n\n  // Source (journal name)\n  const source = findChild(children, 'source');\n  if (source) {\n    parts.push(extractAllText(source.children));\n  }\n\n  // Year, volume, pages\n  const year = findChild(children, 'year');\n  const volume = findChild(children, 'volume');\n  const fpage = findChild(children, 'fpage');\n  const lpage = findChild(children, 'lpage');\n\n  if (year) {\n    let yearStr = extractAllText(year.children);\n    if (volume) {\n      yearStr += `;${extractAllText(volume.children)}`;\n    }\n    if (fpage) {\n      const fpageText = extractAllText(fpage.children);\n      const lpageText = lpage ? extractAllText(lpage.children) : '';\n      yearStr += `:${fpageText}${lpageText ? `-${lpageText}` : ''}`;\n    }\n    parts.push(yearStr);\n  }\n\n  return parts.join('. ') + '.';\n}\n\n/**\n * Extract text from a <mixed-citation>'s children, deduplicating any\n * <pub-id> content that also appears as inline text.\n *\n * Some publishers include the DOI/PMID both as a text node and inside\n * a <pub-id> element, causing duplication like \"10.1234/x 10.1234/x\".\n */\nfunction extractMixedCitationText(children: OrderedNode[]): string {\n  // Collect pub-id values\n  const pubIds = findChildren(children, 'pub-id');\n  const pubIdValues = pubIds\n    .map((p) => extractAllText(p.children).trim())\n    .filter(Boolean);\n\n  if (pubIdValues.length === 0) {\n    return extractAllText(children).trim();\n  }\n\n  // Extract full text\n  const fullText = extractAllText(children).trim();\n\n  // For each pub-id value, if it appears more than once, remove extra occurrences\n  let result = fullText;\n  for (const val of pubIdValues) {\n    // Escape regex special characters\n    const escaped = val.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n    const matches = result.match(new RegExp(escaped, 'g'));\n    if (matches && matches.length > 1) {\n      // Remove the first occurrence (typically the inline text), keep the last (pub-id element)\n      result = result.replace(val, '');\n      // Clean up any leftover extra whitespace\n      result = result.replace(/\\s{2,}/g, ' ').trim();\n    }\n  }\n\n  return result;\n}\n\n/**\n * Extract structured pub-id values (DOI, PMID, PMCID) from children nodes.\n */\nfunction extractPubIds(children: OrderedNode[]): {\n  doi?: string;\n  pmid?: string;\n  pmcid?: string;\n} {\n  const pubIds = findChildren(children, 'pub-id');\n  const result: { doi?: string; pmid?: string; pmcid?: string } = {};\n  for (const p of pubIds) {\n    const idType = p.attrs['pub-id-type'];\n    const value = extractAllText(p.children).trim();\n    if (!value) continue;\n    if (idType === 'doi') result.doi = value;\n    if (idType === 'pmid') result.pmid = value;\n    if (idType === 'pmc' || idType === 'pmcid') {\n      result.pmcid = value.replace(/^PMC/, '');\n    }\n  }\n  return result;\n}\n\n/**\n * Strip extracted pub-id values from reference text to avoid duplication\n * when pub-ids are rendered separately as links.\n */\nfunction stripPubIdValues(\n  text: string,\n  pubIds: { doi?: string; pmid?: string; pmcid?: string },\n): string {\n  let result = text;\n  const values = [pubIds.doi, pubIds.pmid, pubIds.pmcid].filter(Boolean) as string[];\n  for (const val of values) {\n    // Strip common label prefixes (e.g. \"doi: \", \"PMID: \", \"DOI:\", \"pmid:\") followed by the value\n    const escaped = val.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n    result = result.replace(new RegExp(`(?:doi|PMID|pmid|PMC|pmc)[:\\\\s]*${escaped}`, 'gi'), '');\n    // Also strip the bare value itself\n    result = result.replace(new RegExp(escaped, 'g'), '');\n  }\n  // Also strip PMC-prefixed form of pmcid\n  if (pubIds.pmcid) {\n    const pmcFull = `PMC${pubIds.pmcid}`;\n    const escaped = pmcFull.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n    result = result.replace(new RegExp(`(?:pmc|pmcid)[:\\\\s]*${escaped}`, 'gi'), '');\n    result = result.replace(new RegExp(escaped, 'g'), '');\n  }\n  // Clean up trailing/leading whitespace and extra spaces\n  result = result.replace(/\\s{2,}/g, ' ').trim();\n  // Clean up trailing period after stripped content (e.g. \"Title. .\" -> \"Title.\")\n  result = result.replace(/\\.\\s*\\.$/, '.');\n  return result;\n}\n\n/**\n * Parse JATS XML back matter to extract references.\n */\nexport function parseJatsReferences(xml: string): JatsReference[] {\n  const parsed = parser.parse(xml) as OrderedNode[];\n  const article = findArticle(parsed);\n  if (!article) return [];\n\n  const back = findChild(article.children, 'back');\n  if (!back) return [];\n\n  const refList = findChild(back.children, 'ref-list');\n  if (!refList) return [];\n\n  const refs = findChildren(refList.children, 'ref');\n  const references: JatsReference[] = [];\n\n  for (const ref of refs) {\n    const id = ref.attrs['id'] ?? '';\n\n    // Determine the search scope: if <citation-alternatives> exists, search within it;\n    // otherwise search direct children of <ref>\n    const citationAlternatives = findChild(ref.children, 'citation-alternatives');\n    const searchChildren = citationAlternatives ? citationAlternatives.children : ref.children;\n\n    // Try mixed-citation first (already formatted), then element-citation (structured)\n    const mixedCitation = findChild(searchChildren, 'mixed-citation');\n    if (mixedCitation) {\n      const rawText = extractMixedCitationText(mixedCitation.children);\n      const pubIds = extractPubIds(mixedCitation.children);\n      const text = stripPubIdValues(rawText, pubIds);\n      if (id && text) references.push({ id, text, ...pubIds });\n      continue;\n    }\n\n    const elementCitation = findChild(searchChildren, 'element-citation');\n    if (elementCitation) {\n      const rawText = formatElementCitation(elementCitation.children);\n      const pubIds = extractPubIds(elementCitation.children);\n      const text = stripPubIdValues(rawText, pubIds);\n      if (id && text) references.push({ id, text, ...pubIds });\n      continue;\n    }\n\n    // Fallback: extract all text from ref, skipping <label>\n    const childrenWithoutLabel = ref.children.filter((c) => !('label' in c));\n    const text = extractAllText(childrenWithoutLabel).trim();\n    if (id && text) {\n      references.push({ id, text });\n    }\n  }\n\n  return references;\n}\n\n// ─── Back Matter & Floats Parsing ────────────────────────────────────\n\n/** Result of parsing back matter and floats-group. */\nexport interface BackMatterResult {\n  acknowledgments?: string;\n  appendices?: JatsSection[];\n  footnotes?: JatsFootnote[];\n  floats?: BlockElement[];\n  notes?: BackMatterNote[];\n}\n\n/**\n * Parse JATS XML back matter sections (ack, app-group, fn-group)\n * and top-level floats-group.\n */\nexport function parseJatsBackMatter(xml: string): BackMatterResult {\n  const parsed = parser.parse(xml) as OrderedNode[];\n  const article = findArticle(parsed);\n  if (!article) return {};\n\n  const result: BackMatterResult = {};\n\n  // Parse <back> children\n  const back = findChild(article.children, 'back');\n  if (back) {\n    // Acknowledgments: <ack>\n    const ack = findChild(back.children, 'ack');\n    if (ack) {\n      const paragraphs = findChildren(ack.children, 'p');\n      if (paragraphs.length > 0) {\n        result.acknowledgments = paragraphs\n          .map((p) => extractAllText(p.children))\n          .join('\\n\\n');\n      }\n    }\n\n    // Appendices: <app-group>/<app>\n    const appGroup = findChild(back.children, 'app-group');\n    if (appGroup) {\n      const apps = findChildren(appGroup.children, 'app');\n      if (apps.length > 0) {\n        result.appendices = apps.map((app) => parseSection(app.children, 2));\n      }\n    }\n\n    // Footnotes: <fn-group>/<fn>\n    const fnGroup = findChild(back.children, 'fn-group');\n    if (fnGroup) {\n      const fns = findChildren(fnGroup.children, 'fn');\n      if (fns.length > 0) {\n        result.footnotes = fns.map((fn) => {\n          const parts: string[] = [];\n          // Include <title> if present\n          const titleNode = findChild(fn.children, 'title');\n          if (titleNode) {\n            const titleText = extractAllText(titleNode.children).trim();\n            if (titleText) parts.push(titleText);\n          }\n          // Extract text from each <p> separately and join with space\n          const paragraphs = findChildren(fn.children, 'p');\n          for (const p of paragraphs) {\n            const pText = extractAllText(p.children).trim();\n            if (pText) parts.push(pText);\n          }\n          return {\n            id: fn.attrs['id'] ?? '',\n            text: parts.join(' '),\n          };\n        });\n      }\n    }\n\n    // Notes: <notes> (author contributions, funding, data availability, etc.)\n    const notesElements = findChildren(back.children, 'notes');\n    if (notesElements.length > 0) {\n      const notes: BackMatterNote[] = [];\n      for (const note of notesElements) {\n        // Check if this <notes> contains <sec> or nested <notes> children (e.g. Declarations wrapper)\n        const secs = findChildren(note.children, 'sec');\n        const nestedNotes = findChildren(note.children, 'notes');\n        const subItems = secs.length > 0 ? secs : nestedNotes;\n        if (subItems.length > 0) {\n          for (const sub of subItems) {\n            const subTitleNode = findChild(sub.children, 'title');\n            const subTitle = subTitleNode ? extractAllText(subTitleNode.children) : '';\n            const subParagraphs = findChildren(sub.children, 'p');\n            const subText = subParagraphs\n              .map((p) => extractAllText(p.children))\n              .join('\\n\\n');\n            if (subTitle || subText) {\n              notes.push({ title: subTitle, text: subText });\n            }\n          }\n        } else {\n          const titleNode = findChild(note.children, 'title');\n          const title = titleNode ? extractAllText(titleNode.children) : '';\n          const paragraphs = findChildren(note.children, 'p');\n          const text = paragraphs\n            .map((p) => extractAllText(p.children))\n            .join('\\n\\n');\n          if (title || text) {\n            notes.push({ title, text });\n          }\n        }\n      }\n      if (notes.length > 0) {\n        result.notes = notes;\n      }\n    }\n\n    // Glossary: <glossary> (abbreviations, definitions)\n    const glossaryElements = findChildren(back.children, 'glossary');\n    for (const glossary of glossaryElements) {\n      const titleNode = findChild(glossary.children, 'title');\n      const title = titleNode ? extractAllText(titleNode.children) : 'Glossary';\n      const defList = findChild(glossary.children, 'def-list');\n      if (defList) {\n        const defItems = findChildren(defList.children, 'def-item');\n        const lines: string[] = [];\n        for (const item of defItems) {\n          const termNode = findChild(item.children, 'term');\n          const defNode = findChild(item.children, 'def');\n          const term = termNode ? extractAllText(termNode.children) : '';\n          const definition = defNode ? extractAllText(defNode.children) : '';\n          lines.push(`${term}: ${definition}`);\n        }\n        if (!result.notes) result.notes = [];\n        result.notes.push({ title, text: lines.join('\\n') });\n      }\n    }\n  }\n\n  // Floats-group: <floats-group> (sibling of <body> and <back>)\n  const floatsGroup = findChild(article.children, 'floats-group');\n  if (floatsGroup) {\n    const blocks: BlockElement[] = [];\n    for (const child of 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package/dist/fulltext/convert/markdown-writer.d.ts

@@ -1,6 +0,0 @@
-import { JatsDocument } from './types.js';
-/**
- * Convert a parsed JATS document to Markdown string.
- */
-export declare function writeMarkdown(doc: JatsDocument): string;
-//# sourceMappingURL=markdown-writer.d.ts.map

package/dist/fulltext/convert/markdown-writer.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"markdown-writer.d.ts","sourceRoot":"","sources":["../../../src/fulltext/convert/markdown-writer.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,YAAY,EAMb,MAAM,YAAY,CAAC;AAiOpB;;GAEG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,YAAY,GAAG,MAAM,CAuIvD"}

package/dist/fulltext/convert/markdown-writer.js.map

@@ -1 +0,0 @@
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package/dist/fulltext/convert/types.d.ts

@@ -1,141 +0,0 @@
-/**
- * Intermediate representation types for JATS XML to Markdown conversion.
- * These types represent the parsed document structure between parsing and writing.
- */
-/** Author information extracted from JATS contrib-group. */
-export interface JatsAuthor {
-    surname: string;
-    givenNames?: string;
-}
-/** Metadata extracted from JATS front matter. */
-export interface JatsMetadata {
-    title: string;
-    authors: JatsAuthor[];
-    doi?: string;
-    pmcid?: string;
-    pmid?: string;
-    journal?: string;
-    publicationDate?: {
-        year: string;
-        month?: string;
-        day?: string;
-    };
-    volume?: string;
-    issue?: string;
-    pages?: string;
-    keywords?: string[];
-    articleType?: string;
-    license?: string;
-    abstract?: string;
-}
-/** Inline content element (text with optional formatting). */
-export type InlineContent = {
-    type: 'text';
-    text: string;
-} | {
-    type: 'bold';
-    children: InlineContent[];
-} | {
-    type: 'italic';
-    children: InlineContent[];
-} | {
-    type: 'superscript';
-    text: string;
-} | {
-    type: 'subscript';
-    text: string;
-} | {
-    type: 'citation';
-    refId: string;
-    text: string;
-} | {
-    type: 'link';
-    url: string;
-    children: InlineContent[];
-} | {
-    type: 'code';
-    text: string;
-} | {
-    type: 'inline-formula';
-    tex?: string;
-    text: string;
-};
-/** A block-level element within a section. */
-export type BlockElement = {
-    type: 'paragraph';
-    content: InlineContent[];
-} | {
-    type: 'blockquote';
-    content: InlineContent[];
-} | {
-    type: 'list';
-    ordered: boolean;
-    items: InlineContent[][];
-} | {
-    type: 'table';
-    caption?: string;
-    headers: string[];
-    rows: string[][];
-} | {
-    type: 'figure';
-    id?: string;
-    label?: string;
-    caption?: string;
-} | {
-    type: 'boxed-text';
-    title?: string;
-    content: BlockElement[];
-} | {
-    type: 'def-list';
-    title?: string;
-    items: {
-        term: string;
-        definition: string;
-    }[];
-} | {
-    type: 'formula';
-    id?: string;
-    label?: string;
-    tex?: string;
-    text?: string;
-} | {
-    type: 'preformat';
-    text: string;
-};
-/** A document section (may contain nested subsections). */
-export interface JatsSection {
-    title: string;
-    level: number;
-    content: BlockElement[];
-    subsections: JatsSection[];
-}
-/** A reference entry from the back matter. */
-export interface JatsReference {
-    id: string;
-    text: string;
-    doi?: string;
-    pmid?: string;
-    pmcid?: string;
-}
-/** A footnote from back matter fn-group. */
-export interface JatsFootnote {
-    id: string;
-    text: string;
-}
-/** A notes section from back matter (e.g., author contributions, funding). */
-export interface BackMatterNote {
-    title: string;
-    text: string;
-}
-/** Complete parsed JATS document. */
-export interface JatsDocument {
-    metadata: JatsMetadata;
-    sections: JatsSection[];
-    references: JatsReference[];
-    acknowledgments?: string;
-    appendices?: JatsSection[];
-    footnotes?: JatsFootnote[];
-    floats?: BlockElement[];
-    notes?: BackMatterNote[];
-}
-//# sourceMappingURL=types.d.ts.map

package/dist/fulltext/convert/types.d.ts.map

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package/dist/fulltext/discovery/arxiv.d.ts

@@ -1,11 +0,0 @@
-import { OALocation } from '../types';
-/**
- * Check arXiv availability for an article.
- * Since all arXiv articles are freely available, this simply
- * generates the PDF URL from the arXiv ID.
- *
- * @param arxivId - arXiv identifier (e.g., "2401.12345", "hep-ph/9901234")
- * @returns Array with a single PDF OALocation, or null if no ID
- */
-export declare function checkArxiv(arxivId: string): OALocation[] | null;
-//# sourceMappingURL=arxiv.d.ts.map

package/dist/fulltext/discovery/arxiv.d.ts.map

@@ -1 +0,0 @@
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package/dist/fulltext/discovery/arxiv.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"arxiv.js","sources":["../../../src/fulltext/discovery/arxiv.ts"],"sourcesContent":["/**\n * arXiv OA discovery client.\n * Generates PDF download URLs for arXiv articles.\n *\n * URL pattern: https://arxiv.org/pdf/{id}.pdf\n * No API call needed — arXiv is always open access.\n */\n\nimport type { OALocation } from '../types';\n\n/** Strip common prefixes from arXiv IDs */\nfunction normalizeArxivId(id: string): string {\n  return id.replace(/^arXiv:/i, '');\n}\n\n/**\n * Check arXiv availability for an article.\n * Since all arXiv articles are freely available, this simply\n * generates the PDF URL from the arXiv ID.\n *\n * @param arxivId - arXiv identifier (e.g., \"2401.12345\", \"hep-ph/9901234\")\n * @returns Array with a single PDF OALocation, or null if no ID\n */\nexport function checkArxiv(arxivId: string): OALocation[] | null {\n  if (!arxivId) return null;\n\n  const id = normalizeArxivId(arxivId);\n\n  return [\n    {\n      source: 'arxiv',\n      url: `https://arxiv.org/pdf/${id}.pdf`,\n      urlType: 'pdf',\n      version: 'submitted',\n    },\n  ];\n}\n"],"names":[],"mappings":"AAWA,SAAS,iBAAiB,IAAoB;AAC5C,SAAO,GAAG,QAAQ,YAAY,EAAE;AAClC;AAUO,SAAS,WAAW,SAAsC;AAC/D,MAAI,CAAC,QAAS,QAAO;AAErB,QAAM,KAAK,iBAAiB,OAAO;AAEnC,SAAO;AAAA,IACL;AAAA,MACE,QAAQ;AAAA,MACR,KAAK,yBAAyB,EAAE;AAAA,MAChC,SAAS;AAAA,MACT,SAAS;AAAA,IAAA;AAAA,EACX;AAEJ;"}

package/dist/fulltext/discovery/core.d.ts

@@ -1,11 +0,0 @@
-import { OALocation } from '../types';
-/**
- * Check CORE API for Open Access availability of an article.
- *
- * @param doi - The article's DOI
- * @param apiKey - CORE API key (required; returns null if empty)
- * @returns Array of OALocations if found, null if not found or no key
- * @throws On rate limit (429) or network errors
- */
-export declare function checkCore(doi: string, apiKey: string | undefined): Promise<OALocation[] | null>;
-//# sourceMappingURL=core.d.ts.map

package/dist/fulltext/discovery/core.d.ts.map

@@ -1 +0,0 @@
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package/dist/fulltext/discovery/core.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"core.js","sources":["../../../src/fulltext/discovery/core.ts"],"sourcesContent":["/**\n * CORE API OA discovery client.\n * Checks Open Access availability via the CORE API.\n *\n * API: https://api.core.ac.uk/v3/search/works?q=doi:\"{doi}\"\n * Auth: Bearer token (API key, free registration)\n * Rate limit: 10 req/sec\n */\n\nimport type { OALocation } from '../types';\n\nconst CORE_API_BASE = 'https://api.core.ac.uk/v3';\n\n/** CORE API search result shape */\ninterface CoreResult {\n  downloadUrl?: string | null;\n  sourceFulltextUrls?: string[];\n}\n\n/**\n * Check CORE API for Open Access availability of an article.\n *\n * @param doi - The article's DOI\n * @param apiKey - CORE API key (required; returns null if empty)\n * @returns Array of OALocations if found, null if not found or no key\n * @throws On rate limit (429) or network errors\n */\nexport async function checkCore(\n  doi: string,\n  apiKey: string | undefined\n): Promise<OALocation[] | null> {\n  if (!doi) return null;\n  if (!apiKey) return null;\n\n  const url = `${CORE_API_BASE}/search/works?q=doi:\"${doi}\"&limit=1`;\n\n  const response = await fetch(url, {\n    headers: {\n      Authorization: `Bearer ${apiKey}`,\n    },\n  });\n\n  if (!response.ok) {\n    if (response.status === 429) {\n      throw new Error('CORE API rate limit exceeded');\n    }\n    throw new Error(`CORE API error: HTTP ${response.status} ${response.statusText}`);\n  }\n\n  const data = (await response.json()) as {\n    totalHits?: number;\n    results?: CoreResult[];\n  };\n\n  if (!data.totalHits || !data.results || data.results.length === 0) {\n    return null;\n  }\n\n  const firstResult = data.results[0 as number];\n  if (!firstResult) return null;\n\n  // Prefer downloadUrl (direct PDF from CORE)\n  if (firstResult.downloadUrl) {\n    return [\n      {\n        source: 'core',\n        url: firstResult.downloadUrl,\n        urlType: 'pdf',\n        version: 'accepted',\n      },\n    ];\n  }\n\n  // Fall back to sourceFulltextUrls (repository links)\n  if (firstResult.sourceFulltextUrls && firstResult.sourceFulltextUrls.length > 0) {\n    const repoUrl = firstResult.sourceFulltextUrls[0 as number];\n    if (repoUrl) {\n      return [\n        {\n          source: 'core',\n          url: repoUrl,\n          urlType: 'repository',\n          version: 'accepted',\n        },\n      ];\n    }\n  }\n\n  return null;\n}\n"],"names":[],"mappings":"AAWA,MAAM,gBAAgB;AAgBtB,eAAsB,UACpB,KACA,QAC8B;AAC9B,MAAI,CAAC,IAAK,QAAO;AACjB,MAAI,CAAC,OAAQ,QAAO;AAEpB,QAAM,MAAM,GAAG,aAAa,wBAAwB,GAAG;AAEvD,QAAM,WAAW,MAAM,MAAM,KAAK;AAAA,IAChC,SAAS;AAAA,MACP,eAAe,UAAU,MAAM;AAAA,IAAA;AAAA,EACjC,CACD;AAED,MAAI,CAAC,SAAS,IAAI;AAChB,QAAI,SAAS,WAAW,KAAK;AAC3B,YAAM,IAAI,MAAM,8BAA8B;AAAA,IAChD;AACA,UAAM,IAAI,MAAM,wBAAwB,SAAS,MAAM,IAAI,SAAS,UAAU,EAAE;AAAA,EAClF;AAEA,QAAM,OAAQ,MAAM,SAAS,KAAA;AAK7B,MAAI,CAAC,KAAK,aAAa,CAAC,KAAK,WAAW,KAAK,QAAQ,WAAW,GAAG;AACjE,WAAO;AAAA,EACT;AAEA,QAAM,cAAc,KAAK,QAAQ,CAAW;AAC5C,MAAI,CAAC,YAAa,QAAO;AAGzB,MAAI,YAAY,aAAa;AAC3B,WAAO;AAAA,MACL;AAAA,QACE,QAAQ;AAAA,QACR,KAAK,YAAY;AAAA,QACjB,SAAS;AAAA,QACT,SAAS;AAAA,MAAA;AAAA,IACX;AAAA,EAEJ;AAGA,MAAI,YAAY,sBAAsB,YAAY,mBAAmB,SAAS,GAAG;AAC/E,UAAM,UAAU,YAAY,mBAAmB,CAAW;AAC1D,QAAI,SAAS;AACX,aAAO;AAAA,QACL;AAAA,UACE,QAAQ;AAAA,UACR,KAAK;AAAA,UACL,SAAS;AAAA,UACT,SAAS;AAAA,QAAA;AAAA,MACX;AAAA,IAEJ;AAAA,EACF;AAEA,SAAO;AACT;"}

package/dist/fulltext/discovery/index.d.ts

@@ -1,28 +0,0 @@
-import { OALocation, OAStatus } from '../types';
-export interface DiscoveryArticle {
-    doi?: string;
-    pmid?: string;
-    pmcid?: string;
-    arxivId?: string;
-}
-export interface DiscoveryConfig {
-    unpaywallEmail: string;
-    coreApiKey: string;
-    preferSources: string[];
-}
-export interface DiscoveryResult {
-    oaStatus: OAStatus;
-    locations: OALocation[];
-    errors: Array<{
-        source: string;
-        error: string;
-    }>;
-}
-/**
- * Discover OA availability for an article across all configured sources.
- * Checks sources in the order specified by config.preferSources, falling back
- * to the default order. Individual source errors are caught and reported
- * without failing the whole discovery.
- */
-export declare function discoverOA(article: DiscoveryArticle, config: DiscoveryConfig): Promise<DiscoveryResult>;
-//# sourceMappingURL=index.d.ts.map

package/dist/fulltext/discovery/index.d.ts.map

@@ -1 +0,0 @@
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package/dist/fulltext/discovery/index.js

@@ -1,75 +0,0 @@
-import { checkUnpaywall } from "./unpaywall.js";
-import { checkPmc } from "./pmc.js";
-import { checkArxiv } from "./arxiv.js";
-import { checkCore } from "./core.js";
-const DEFAULT_SOURCE_ORDER = ["pmc", "arxiv", "unpaywall", "core"];
-async function discoverOA(article, config) {
-  const locations = [];
-  const errors = [];
-  let sourcesChecked = 0;
-  const sourceOrder = config.preferSources.length > 0 ? config.preferSources : DEFAULT_SOURCE_ORDER;
-  for (const source of sourceOrder) {
-    switch (source) {
-      case "pmc":
-        if (article.pmid || article.pmcid) {
-          sourcesChecked++;
-          try {
-            const ids = {};
-            if (article.pmid) ids.pmid = article.pmid;
-            if (article.pmcid) ids.pmcid = article.pmcid;
-            const pmcResult = await checkPmc(ids);
-            if (pmcResult) locations.push(...pmcResult);
-          } catch (err) {
-            errors.push({ source: "pmc", error: String(err) });
-          }
-        }
-        break;
-      case "arxiv":
-        if (article.arxivId) {
-          sourcesChecked++;
-          try {
-            const arxivResult = checkArxiv(article.arxivId);
-            if (arxivResult) locations.push(...arxivResult);
-          } catch (err) {
-            errors.push({ source: "arxiv", error: String(err) });
-          }
-        }
-        break;
-      case "unpaywall":
-        if (config.unpaywallEmail && article.doi) {
-          sourcesChecked++;
-          try {
-            const unpaywallResult = await checkUnpaywall(article.doi, config.unpaywallEmail);
-            if (unpaywallResult) locations.push(...unpaywallResult);
-          } catch (err) {
-            errors.push({ source: "unpaywall", error: String(err) });
-          }
-        }
-        break;
-      case "core":
-        if (config.coreApiKey && article.doi) {
-          sourcesChecked++;
-          try {
-            const coreResult = await checkCore(article.doi, config.coreApiKey);
-            if (coreResult) locations.push(...coreResult);
-          } catch (err) {
-            errors.push({ source: "core", error: String(err) });
-          }
-        }
-        break;
-    }
-  }
-  let oaStatus;
-  if (locations.length > 0) {
-    oaStatus = "open";
-  } else if (errors.length > 0 && errors.length >= sourcesChecked) {
-    oaStatus = "unknown";
-  } else {
-    oaStatus = "closed";
-  }
-  return { oaStatus, locations, errors };
-}
-export {
-  discoverOA
-};
-//# sourceMappingURL=index.js.map

package/dist/fulltext/discovery/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sources":["../../../src/fulltext/discovery/index.ts"],"sourcesContent":["/**\n * OA Discovery Aggregator.\n * Combines results from multiple OA discovery sources.\n */\n\nimport type { OALocation, OAStatus } from '../types';\nimport { checkUnpaywall } from './unpaywall';\nimport { checkPmc } from './pmc';\nimport { checkArxiv } from './arxiv';\nimport { checkCore } from './core';\n\nexport interface DiscoveryArticle {\n  doi?: string;\n  pmid?: string;\n  pmcid?: string;\n  arxivId?: string;\n}\n\nexport interface DiscoveryConfig {\n  unpaywallEmail: string;\n  coreApiKey: string;\n  preferSources: string[];\n}\n\nexport interface DiscoveryResult {\n  oaStatus: OAStatus;\n  locations: OALocation[];\n  errors: Array<{ source: string; error: string }>;\n}\n\n/** Default source order when preferSources is empty or not specified */\nconst DEFAULT_SOURCE_ORDER = ['pmc', 'arxiv', 'unpaywall', 'core'];\n\n/**\n * Discover OA availability for an article across all configured sources.\n * Checks sources in the order specified by config.preferSources, falling back\n * to the default order. Individual source errors are caught and reported\n * without failing the whole discovery.\n */\nexport async function discoverOA(\n  article: DiscoveryArticle,\n  config: DiscoveryConfig\n): Promise<DiscoveryResult> {\n  const locations: OALocation[] = [];\n  const errors: Array<{ source: string; error: string }> = [];\n  let sourcesChecked = 0;\n\n  const sourceOrder =\n    config.preferSources.length > 0 ? config.preferSources : DEFAULT_SOURCE_ORDER;\n\n  for (const source of sourceOrder) {\n    switch (source) {\n      case 'pmc':\n        if (article.pmid || article.pmcid) {\n          sourcesChecked++;\n          try {\n            const ids: { pmid?: string; pmcid?: string } = {};\n            if (article.pmid) ids.pmid = article.pmid;\n            if (article.pmcid) ids.pmcid = article.pmcid;\n            const pmcResult = await checkPmc(ids);\n            if (pmcResult) locations.push(...pmcResult);\n          } catch (err) {\n            errors.push({ source: 'pmc', error: String(err) });\n          }\n        }\n        break;\n\n      case 'arxiv':\n        if (article.arxivId) {\n          sourcesChecked++;\n          try {\n            const arxivResult = checkArxiv(article.arxivId);\n            if (arxivResult) locations.push(...arxivResult);\n          } catch (err) {\n            errors.push({ source: 'arxiv', error: String(err) });\n          }\n        }\n        break;\n\n      case 'unpaywall':\n        if (config.unpaywallEmail && article.doi) {\n          sourcesChecked++;\n          try {\n            const unpaywallResult = await checkUnpaywall(article.doi, config.unpaywallEmail);\n            if (unpaywallResult) locations.push(...unpaywallResult);\n          } catch (err) {\n            errors.push({ source: 'unpaywall', error: String(err) });\n          }\n        }\n        break;\n\n      case 'core':\n        if (config.coreApiKey && article.doi) {\n          sourcesChecked++;\n          try {\n            const coreResult = await checkCore(article.doi, config.coreApiKey);\n            if (coreResult) locations.push(...coreResult);\n          } catch (err) {\n            errors.push({ source: 'core', error: String(err) });\n          }\n        }\n        break;\n    }\n  }\n\n  // Determine OA status\n  let oaStatus: OAStatus;\n  if (locations.length > 0) {\n    oaStatus = 'open';\n  } else if (errors.length > 0 && errors.length >= sourcesChecked) {\n    // All checked sources errored — we can't determine status\n    oaStatus = 'unknown';\n  } else {\n    oaStatus = 'closed';\n  }\n\n  return { oaStatus, locations, errors };\n}\n"],"names":[],"mappings":";;;;AA+BA,MAAM,uBAAuB,CAAC,OAAO,SAAS,aAAa,MAAM;AAQjE,eAAsB,WACpB,SACA,QAC0B;AAC1B,QAAM,YAA0B,CAAA;AAChC,QAAM,SAAmD,CAAA;AACzD,MAAI,iBAAiB;AAErB,QAAM,cACJ,OAAO,cAAc,SAAS,IAAI,OAAO,gBAAgB;AAE3D,aAAW,UAAU,aAAa;AAChC,YAAQ,QAAA;AAAA,MACN,KAAK;AACH,YAAI,QAAQ,QAAQ,QAAQ,OAAO;AACjC;AACA,cAAI;AACF,kBAAM,MAAyC,CAAA;AAC/C,gBAAI,QAAQ,KAAM,KAAI,OAAO,QAAQ;AACrC,gBAAI,QAAQ,MAAO,KAAI,QAAQ,QAAQ;AACvC,kBAAM,YAAY,MAAM,SAAS,GAAG;AACpC,gBAAI,UAAW,WAAU,KAAK,GAAG,SAAS;AAAA,UAC5C,SAAS,KAAK;AACZ,mBAAO,KAAK,EAAE,QAAQ,OAAO,OAAO,OAAO,GAAG,GAAG;AAAA,UACnD;AAAA,QACF;AACA;AAAA,MAEF,KAAK;AACH,YAAI,QAAQ,SAAS;AACnB;AACA,cAAI;AACF,kBAAM,cAAc,WAAW,QAAQ,OAAO;AAC9C,gBAAI,YAAa,WAAU,KAAK,GAAG,WAAW;AAAA,UAChD,SAAS,KAAK;AACZ,mBAAO,KAAK,EAAE,QAAQ,SAAS,OAAO,OAAO,GAAG,GAAG;AAAA,UACrD;AAAA,QACF;AACA;AAAA,MAEF,KAAK;AACH,YAAI,OAAO,kBAAkB,QAAQ,KAAK;AACxC;AACA,cAAI;AACF,kBAAM,kBAAkB,MAAM,eAAe,QAAQ,KAAK,OAAO,cAAc;AAC/E,gBAAI,gBAAiB,WAAU,KAAK,GAAG,eAAe;AAAA,UACxD,SAAS,KAAK;AACZ,mBAAO,KAAK,EAAE,QAAQ,aAAa,OAAO,OAAO,GAAG,GAAG;AAAA,UACzD;AAAA,QACF;AACA;AAAA,MAEF,KAAK;AACH,YAAI,OAAO,cAAc,QAAQ,KAAK;AACpC;AACA,cAAI;AACF,kBAAM,aAAa,MAAM,UAAU,QAAQ,KAAK,OAAO,UAAU;AACjE,gBAAI,WAAY,WAAU,KAAK,GAAG,UAAU;AAAA,UAC9C,SAAS,KAAK;AACZ,mBAAO,KAAK,EAAE,QAAQ,QAAQ,OAAO,OAAO,GAAG,GAAG;AAAA,UACpD;AAAA,QACF;AACA;AAAA,IAAA;AAAA,EAEN;AAGA,MAAI;AACJ,MAAI,UAAU,SAAS,GAAG;AACxB,eAAW;AAAA,EACb,WAAW,OAAO,SAAS,KAAK,OAAO,UAAU,gBAAgB;AAE/D,eAAW;AAAA,EACb,OAAO;AACL,eAAW;AAAA,EACb;AAEA,SAAO,EAAE,UAAU,WAAW,OAAA;AAChC;"}

package/dist/fulltext/discovery/pmc.d.ts

@@ -1,19 +0,0 @@
-import { OALocation } from '../types';
-export interface PmcIdentifiers {
-    pmid?: string;
-    pmcid?: string;
-}
-export interface PmcOptions {
-    apiKey?: string;
-}
-/**
- * Generate PMC download URLs from a known PMCID.
- */
-export declare function getPmcUrls(pmcid: string): OALocation[];
-/**
- * Check PMC availability for an article.
- * If PMCID is known, generates URLs directly.
- * If only PMID is known, looks up PMCID via E-utilities elink.
- */
-export declare function checkPmc(ids: PmcIdentifiers, options?: PmcOptions): Promise<OALocation[] | null>;
-//# sourceMappingURL=pmc.d.ts.map

package/dist/fulltext/discovery/pmc.d.ts.map

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package/dist/fulltext/discovery/pmc.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"pmc.js","sources":["../../../src/fulltext/discovery/pmc.ts"],"sourcesContent":["/**\n * PMC OA discovery client.\n * Checks PubMed Central availability and generates download URLs.\n *\n * PDF: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{id}/pdf/\n * XML: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id={pmcid}&rettype=xml\n * PMID→PMCID: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&id={pmid}&retmode=json\n */\n\nimport type { OALocation } from '../types';\n\nconst EUTILS_BASE = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';\n\nexport interface PmcIdentifiers {\n  pmid?: string;\n  pmcid?: string;\n}\n\nexport interface PmcOptions {\n  apiKey?: string;\n}\n\n/** Strip \"PMC\" prefix from PMCID, returning just the numeric part */\nfunction stripPmcPrefix(pmcid: string): string {\n  return pmcid.replace(/^PMC/i, '');\n}\n\n/** Ensure PMCID has the \"PMC\" prefix */\nfunction ensurePmcPrefix(pmcid: string): string {\n  return pmcid.startsWith('PMC') ? pmcid : `PMC${pmcid}`;\n}\n\n/**\n * Generate PMC download URLs from a known PMCID.\n */\nexport function getPmcUrls(pmcid: string): OALocation[] {\n  const numericId = stripPmcPrefix(pmcid);\n  const fullPmcid = ensurePmcPrefix(pmcid);\n\n  return [\n    {\n      source: 'pmc',\n      url: `https://www.ncbi.nlm.nih.gov/pmc/articles/${fullPmcid}/pdf/`,\n      urlType: 'pdf',\n      version: 'published',\n    },\n    {\n      source: 'pmc',\n      url: `${EUTILS_BASE}/efetch.fcgi?db=pmc&id=${numericId}&rettype=xml`,\n      urlType: 'xml',\n      version: 'published',\n    },\n  ];\n}\n\n/**\n * Look up PMCID from PMID via E-utilities elink API.\n * @returns PMCID string or null if not in PMC\n */\nasync function lookupPmcid(pmid: string, options?: PmcOptions): Promise<string | null> {\n  let url = `${EUTILS_BASE}/elink.fcgi?dbfrom=pubmed&db=pmc&id=${pmid}&retmode=json`;\n  if (options?.apiKey) {\n    url += `&api_key=${options.apiKey}`;\n  }\n\n  const response = await fetch(url);\n  if (!response.ok) {\n    throw new Error(`PMC elink API error: HTTP ${response.status}`);\n  }\n\n  const data = (await response.json()) as {\n    linksets?: Array<{\n      linksetdbs?: Array<{\n        dbto: string;\n        links?: string[];\n      }>;\n    }>;\n  };\n\n  const linksets = data.linksets;\n  if (!linksets || linksets.length === 0) return null;\n\n  const firstLinkset = linksets[0 as number];\n  if (!firstLinkset?.linksetdbs) return null;\n\n  const pmcLink = firstLinkset.linksetdbs.find((db) => db.dbto === 'pmc');\n  if (!pmcLink?.links || pmcLink.links.length === 0) return null;\n\n  const pmcNumericId = pmcLink.links[0 as number];\n  return pmcNumericId ? `PMC${pmcNumericId}` : null;\n}\n\n/**\n * Check PMC availability for an article.\n * If PMCID is known, generates URLs directly.\n * If only PMID is known, looks up PMCID via E-utilities elink.\n */\nexport async function checkPmc(\n  ids: PmcIdentifiers,\n  options?: PmcOptions\n): Promise<OALocation[] | null> {\n  // If PMCID is already known, generate URLs directly\n  if (ids.pmcid) {\n    return getPmcUrls(ids.pmcid);\n  }\n\n  // If only PMID is known, look up PMCID\n  if (ids.pmid) {\n    const pmcid = await lookupPmcid(ids.pmid, options);\n    if (!pmcid) return null;\n    return getPmcUrls(pmcid);\n  }\n\n  // No identifiers provided\n  return null;\n}\n"],"names":[],"mappings":"AAWA,MAAM,cAAc;AAYpB,SAAS,eAAe,OAAuB;AAC7C,SAAO,MAAM,QAAQ,SAAS,EAAE;AAClC;AAGA,SAAS,gBAAgB,OAAuB;AAC9C,SAAO,MAAM,WAAW,KAAK,IAAI,QAAQ,MAAM,KAAK;AACtD;AAKO,SAAS,WAAW,OAA6B;AACtD,QAAM,YAAY,eAAe,KAAK;AACtC,QAAM,YAAY,gBAAgB,KAAK;AAEvC,SAAO;AAAA,IACL;AAAA,MACE,QAAQ;AAAA,MACR,KAAK,6CAA6C,SAAS;AAAA,MAC3D,SAAS;AAAA,MACT,SAAS;AAAA,IAAA;AAAA,IAEX;AAAA,MACE,QAAQ;AAAA,MACR,KAAK,GAAG,WAAW,0BAA0B,SAAS;AAAA,MACtD,SAAS;AAAA,MACT,SAAS;AAAA,IAAA;AAAA,EACX;AAEJ;AAMA,eAAe,YAAY,MAAc,SAA8C;AACrF,MAAI,MAAM,GAAG,WAAW,uCAAuC,IAAI;AAKnE,QAAM,WAAW,MAAM,MAAM,GAAG;AAChC,MAAI,CAAC,SAAS,IAAI;AAChB,UAAM,IAAI,MAAM,6BAA6B,SAAS,MAAM,EAAE;AAAA,EAChE;AAEA,QAAM,OAAQ,MAAM,SAAS,KAAA;AAS7B,QAAM,WAAW,KAAK;AACtB,MAAI,CAAC,YAAY,SAAS,WAAW,EAAG,QAAO;AAE/C,QAAM,eAAe,SAAS,CAAW;AACzC,MAAI,CAAC,cAAc,WAAY,QAAO;AAEtC,QAAM,UAAU,aAAa,WAAW,KAAK,CAAC,OAAO,GAAG,SAAS,KAAK;AACtE,MAAI,CAAC,SAAS,SAAS,QAAQ,MAAM,WAAW,EAAG,QAAO;AAE1D,QAAM,eAAe,QAAQ,MAAM,CAAW;AAC9C,SAAO,eAAe,MAAM,YAAY,KAAK;AAC/C;AAOA,eAAsB,SACpB,KACA,SAC8B;AAE9B,MAAI,IAAI,OAAO;AACb,WAAO,WAAW,IAAI,KAAK;AAAA,EAC7B;AAGA,MAAI,IAAI,MAAM;AACZ,UAAM,QAAQ,MAAM,YAAY,IAAI,IAAa;AACjD,QAAI,CAAC,MAAO,QAAO;AACnB,WAAO,WAAW,KAAK;AAAA,EACzB;AAGA,SAAO;AACT;"}

package/dist/fulltext/discovery/unpaywall.d.ts

@@ -1,11 +0,0 @@
-import { OALocation } from '../types';
-/**
- * Check Unpaywall for Open Access availability of an article.
- *
- * @param doi - The article's DOI
- * @param email - Email address required by Unpaywall API (free, no registration)
- * @returns Array of OALocations if OA, null if closed/not found
- * @throws On rate limit (429) or network errors
- */
-export declare function checkUnpaywall(doi: string, email: string): Promise<OALocation[] | null>;
-//# sourceMappingURL=unpaywall.d.ts.map

package/dist/fulltext/discovery/unpaywall.d.ts.map

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package/dist/fulltext/discovery/unpaywall.js.map

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-{"version":3,"file":"unpaywall.js","sources":["../../../src/fulltext/discovery/unpaywall.ts"],"sourcesContent":["/**\n * Unpaywall OA discovery client.\n * Checks Open Access availability via the Unpaywall API.\n *\n * API: https://api.unpaywall.org/v2/{doi}?email={email}\n * Rate limit: 100,000 requests/day (no per-second limit documented)\n */\n\nimport type { OALocation } from '../types';\n\nconst UNPAYWALL_BASE_URL = 'https://api.unpaywall.org/v2';\n\n/** Unpaywall API response location shape */\ninterface UnpaywallLocation {\n  url_for_pdf?: string | null;\n  url_for_landing_page?: string | null;\n  license?: string | null;\n  version?: string | null;\n  host_type?: string | null;\n}\n\n/** Map Unpaywall version strings to our OALocation version format */\nfunction mapVersion(version: string | null | undefined): OALocation['version'] {\n  switch (version) {\n    case 'publishedVersion':\n      return 'published';\n    case 'acceptedVersion':\n      return 'accepted';\n    case 'submittedVersion':\n      return 'submitted';\n    default:\n      return 'published';\n  }\n}\n\n/** Convert an Unpaywall location to our OALocation format */\nfunction toOALocation(loc: UnpaywallLocation): OALocation | null {\n  const hasPdf = loc.url_for_pdf != null;\n  const url = hasPdf ? loc.url_for_pdf : loc.url_for_landing_page;\n  if (!url) return null;\n\n  const result: OALocation = {\n    source: 'unpaywall',\n    url,\n    urlType: hasPdf ? 'pdf' : 'html',\n    version: mapVersion(loc.version),\n  };\n  if (loc.license) {\n    result.license = loc.license;\n  }\n  return result;\n}\n\n/**\n * Check Unpaywall for Open Access availability of an article.\n *\n * @param doi - The article's DOI\n * @param email - Email address required by Unpaywall API (free, no registration)\n * @returns Array of OALocations if OA, null if closed/not found\n * @throws On rate limit (429) or network errors\n */\nexport async function checkUnpaywall(\n  doi: string,\n  email: string\n): Promise<OALocation[] | null> {\n  if (!doi) return null;\n\n  if (!email) {\n    throw new Error('Unpaywall email is required for API access');\n  }\n\n  const url = `${UNPAYWALL_BASE_URL}/${doi}?email=${encodeURIComponent(email)}`;\n\n  const response = await fetch(url);\n\n  if (!response.ok) {\n    if (response.status === 404) return null;\n    if (response.status === 429) {\n      throw new Error('Unpaywall rate limit exceeded');\n    }\n    throw new Error(`Unpaywall API error: HTTP ${response.status} ${response.statusText}`);\n  }\n\n  const data = (await response.json()) as {\n    is_oa?: boolean;\n    oa_locations?: UnpaywallLocation[];\n  };\n\n  if (!data.is_oa || !data.oa_locations || data.oa_locations.length === 0) {\n    return null;\n  }\n\n  const locations: OALocation[] = [];\n  for (const loc of data.oa_locations) {\n    const oaLoc = toOALocation(loc);\n    if (oaLoc) locations.push(oaLoc);\n  }\n\n  return locations.length > 0 ? locations : null;\n}\n"],"names":[],"mappings":"AAUA,MAAM,qBAAqB;AAY3B,SAAS,WAAW,SAA2D;AAC7E,UAAQ,SAAA;AAAA,IACN,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT;AACE,aAAO;AAAA,EAAA;AAEb;AAGA,SAAS,aAAa,KAA2C;AAC/D,QAAM,SAAS,IAAI,eAAe;AAClC,QAAM,MAAM,SAAS,IAAI,cAAc,IAAI;AAC3C,MAAI,CAAC,IAAK,QAAO;AAEjB,QAAM,SAAqB;AAAA,IACzB,QAAQ;AAAA,IACR;AAAA,IACA,SAAS,SAAS,QAAQ;AAAA,IAC1B,SAAS,WAAW,IAAI,OAAO;AAAA,EAAA;AAEjC,MAAI,IAAI,SAAS;AACf,WAAO,UAAU,IAAI;AAAA,EACvB;AACA,SAAO;AACT;AAUA,eAAsB,eACpB,KACA,OAC8B;AAC9B,MAAI,CAAC,IAAK,QAAO;AAEjB,MAAI,CAAC,OAAO;AACV,UAAM,IAAI,MAAM,4CAA4C;AAAA,EAC9D;AAEA,QAAM,MAAM,GAAG,kBAAkB,IAAI,GAAG,UAAU,mBAAmB,KAAK,CAAC;AAE3E,QAAM,WAAW,MAAM,MAAM,GAAG;AAEhC,MAAI,CAAC,SAAS,IAAI;AAChB,QAAI,SAAS,WAAW,IAAK,QAAO;AACpC,QAAI,SAAS,WAAW,KAAK;AAC3B,YAAM,IAAI,MAAM,+BAA+B;AAAA,IACjD;AACA,UAAM,IAAI,MAAM,6BAA6B,SAAS,MAAM,IAAI,SAAS,UAAU,EAAE;AAAA,EACvF;AAEA,QAAM,OAAQ,MAAM,SAAS,KAAA;AAK7B,MAAI,CAAC,KAAK,SAAS,CAAC,KAAK,gBAAgB,KAAK,aAAa,WAAW,GAAG;AACvE,WAAO;AAAA,EACT;AAEA,QAAM,YAA0B,CAAA;AAChC,aAAW,OAAO,KAAK,cAAc;AACnC,UAAM,QAAQ,aAAa,GAAG;AAC9B,QAAI,MAAO,WAAU,KAAK,KAAK;AAAA,EACjC;AAEA,SAAO,UAAU,SAAS,IAAI,YAAY;AAC5C;"}