npm - @ncukondo/search-hub - Versions diffs - 0.12.0 → 0.12.2 - Mend

@ncukondo/search-hub 0.12.0 → 0.12.2

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package/dist/node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js.map ADDED Viewed

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+ {"version":3,"file":"jats-parser.js","sources":["../../../../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js"],"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 */\nimport { XMLParser } from \"fast-xml-parser\";\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// ─── Navigation Helpers ──────────────────────────────────────────────\n/** Get the tag name of an ordered node (the first key that isn't \":@\" or \"#text\"). */\nfunction getTagName(node) {\n for (const key of Object.keys(node)) {\n if (key !== \":@\" && key !== \"#text\")\n return key;\n }\n return undefined;\n}\n/** Get the children array of an element node. */\nfunction getChildren(node) {\n const tag = getTagName(node);\n if (!tag)\n return [];\n const children = node[tag];\n return Array.isArray(children) ? children : [];\n}\n/** Get attributes of an element node. */\nfunction getAttr(node, attrName) {\n const attrs = node[\":@\"];\n if (!attrs)\n return undefined;\n const val = attrs[`@_${attrName}`];\n return val != null ? String(val) : undefined;\n}\n/** Get all attributes of an element node (strips @_ prefix for consistency with getAttr). */\nfunction getAttrs(node) {\n const attrs = node[\":@\"];\n if (!attrs)\n return {};\n const result = {};\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/** Find the first child element with the given tag name. */\nfunction findChild(children, tagName) {\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 : [],\n attrs: getAttrs(child),\n };\n }\n }\n return undefined;\n}\n/** Find all child elements with the given tag name. */\nfunction findChildren(children, tagName) {\n const results = [];\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 : [],\n attrs: getAttrs(child),\n });\n }\n }\n return results;\n}\n/** Get text content from a #text node. */\nfunction getTextContent(child) {\n if (\"#text\" in child) {\n const val = child[\"#text\"];\n return val != null ? String(val) : undefined;\n }\n return undefined;\n}\n/**\n * Find the <article> element, handling optional <pmc-articleset> wrapper\n * that appears in efetch responses.\n */\nfunction findArticle(parsed) {\n const direct = findChild(parsed, \"article\");\n if (direct)\n return direct;\n const wrapper = findChild(parsed, \"pmc-articleset\");\n if (wrapper)\n return findChild(wrapper.children, \"article\");\n return undefined;\n}\n// ─── Text Extraction ─────────────────────────────────────────────────\n/** Tags whose text content should be followed by a space when adjacent to other content. */\nconst SPACE_AFTER_TAGS = new Set([\"surname\", \"given-names\", \"name\", \"string-name\"]);\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) {\n if (node == null)\n return \"\";\n if (typeof node === \"string\")\n return node;\n if (typeof node === \"number\")\n return String(node);\n if (Array.isArray(node)) {\n return joinChildTexts(node);\n }\n if (typeof node === \"object\") {\n const obj = node;\n // Text node\n const text = getTextContent(obj);\n if (text != null)\n 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);\n }\n }\n }\n return \"\";\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) {\n const parts = [];\n for (const child of children) {\n const text = extractAllText(child);\n if (!text)\n continue;\n const tag = getTagName(child);\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.at(-1);\n if (prev && !/[\\s,;.:()\\-/]$/.test(prev)) {\n parts.push(\" \");\n }\n }\n parts.push(text);\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// ─── Metadata Parsing ────────────────────────────────────────────────\n/** Extract DOI, PMCID, and PMID from article-id elements. */\nfunction parseArticleIds(metaChildren) {\n const articleIds = findChildren(metaChildren, \"article-id\");\n const result = {};\n for (const idEntry of articleIds) {\n const idType = idEntry.attrs[\"pub-id-type\"];\n const idText = extractAllText(idEntry.children);\n if (idType === \"doi\")\n result.doi = idText;\n if (idType === \"pmc\" || idType === \"pmcid\") {\n result.pmcid = idText.replace(/^PMC/, \"\");\n }\n if (idType === \"pmid\")\n result.pmid = idText;\n }\n return result;\n}\n/** Extract authors from contrib-group. */\nfunction parseAuthors(metaChildren) {\n const authors = [];\n const contribGroup = findChild(metaChildren, \"contrib-group\");\n if (!contribGroup)\n return authors;\n const contribs = findChildren(contribGroup.children, \"contrib\");\n for (const contrib of contribs) {\n if (contrib.attrs[\"contrib-type\"] !== \"author\")\n continue;\n const nameNode = findChild(contrib.children, \"name\");\n if (!nameNode)\n continue;\n const surnameNode = findChild(nameNode.children, \"surname\");\n const givenNamesNode = findChild(nameNode.children, \"given-names\");\n const author = {\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 return authors;\n}\n/** Extract abstract text, handling both structured and simple formats. */\nfunction parseAbstract(metaChildren) {\n const abstractNode = findChild(metaChildren, \"abstract\");\n if (!abstractNode)\n return undefined;\n // Structured abstract with <sec> elements\n const sections = findChildren(abstractNode.children, \"sec\");\n if (sections.length > 0) {\n return parseStructuredAbstract(sections);\n }\n // Simple abstract with <p>\n const paragraphs = findChildren(abstractNode.children, \"p\");\n if (paragraphs.length > 0) {\n return paragraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n }\n const text = extractAllText(abstractNode.children);\n return text || undefined;\n}\n/** Parse a structured abstract with <sec> elements. */\nfunction parseStructuredAbstract(sections) {\n const parts = [];\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 parts.push(secTitle ? `${secTitle}: ${text}` : text);\n }\n return parts.join(\"\\n\\n\");\n}\n/** Extract a date from a pub-date node. */\nfunction extractDateFromNode(pd) {\n const yearNode = findChild(pd.children, \"year\");\n if (!yearNode)\n return undefined;\n const year = extractAllText(yearNode.children);\n const monthNode = findChild(pd.children, \"month\");\n const dayNode = findChild(pd.children, \"day\");\n const date = { year };\n if (monthNode)\n date.month = extractAllText(monthNode.children);\n if (dayNode)\n date.day = extractAllText(dayNode.children);\n return date;\n}\n/**\n * Extract publication date with priority: epub > ppub > collection > any other.\n * Falls back to first available date if none match priority.\n */\nfunction parsePublicationDate(metaChildren) {\n const pubDates = findChildren(metaChildren, \"pub-date\");\n const datePriority = { epub: 0, ppub: 1, collection: 2 };\n let bestPriority = Number.POSITIVE_INFINITY;\n let publicationDate;\n for (const pd of pubDates) {\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 publicationDate = extractDateFromNode(pd);\n }\n }\n // If no prioritized date found, take first available\n if (!publicationDate && pubDates.length > 0) {\n const pd = pubDates.at(0);\n if (pd) {\n publicationDate = extractDateFromNode(pd);\n }\n }\n return publicationDate;\n}\n/** Extract license information from permissions. */\nfunction parseLicense(metaChildren) {\n const permissions = findChild(metaChildren, \"permissions\");\n if (!permissions)\n return undefined;\n const licenseNode = findChild(permissions.children, \"license\");\n if (!licenseNode)\n return undefined;\n // Prefer @xlink:href (standardized URL) over <license-p> (free-text)\n const href = licenseNode.attrs[\"xlink:href\"];\n if (href)\n return href;\n const licenseP = findChild(licenseNode.children, \"license-p\");\n if (licenseP)\n return extractAllText(licenseP.children).trim();\n return undefined;\n}\n/** Extract keywords from all kwd-group elements. */\nfunction parseKeywords(metaChildren) {\n const kwdGroups = findChildren(metaChildren, \"kwd-group\");\n const keywords = [];\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)\n keywords.push(text);\n }\n }\n return keywords;\n}\n/** Extract volume, issue, and pages from article meta. */\nfunction parseVolumeAndPages(metaChildren) {\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;\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 }\n else {\n const elocationNode = findChild(metaChildren, \"elocation-id\");\n if (elocationNode)\n pages = extractAllText(elocationNode.children);\n }\n const result = {};\n if (volume !== undefined)\n result.volume = volume;\n if (issue !== undefined)\n result.issue = issue;\n if (pages !== undefined)\n result.pages = pages;\n return result;\n}\n/** Extract journal name from front matter journal-meta. */\nfunction parseJournalName(frontChildren) {\n const journalMeta = findChild(frontChildren, \"journal-meta\");\n if (!journalMeta)\n return undefined;\n const titleGroup = findChild(journalMeta.children, \"journal-title-group\");\n if (titleGroup) {\n const jTitle = findChild(titleGroup.children, \"journal-title\");\n if (jTitle)\n return extractAllText(jTitle.children);\n }\n const jTitle = findChild(journalMeta.children, \"journal-title\");\n if (jTitle)\n return extractAllText(jTitle.children);\n return undefined;\n}\n/** Extract article title from title-group. */\nfunction parseArticleTitle(metaChildren) {\n const titleGroup = findChild(metaChildren, \"title-group\");\n const articleTitle = titleGroup ? findChild(titleGroup.children, \"article-title\") : undefined;\n return articleTitle ? extractAllText(articleTitle.children) : \"\";\n}\n/** Assemble optional metadata fields into a JatsMetadata result. */\nfunction assembleMetadata(base, fields) {\n const result = { ...base };\n if (fields.doi)\n result.doi = fields.doi;\n if (fields.pmcid)\n result.pmcid = fields.pmcid;\n if (fields.pmid)\n result.pmid = fields.pmid;\n if (fields.journal)\n result.journal = fields.journal;\n if (fields.publicationDate)\n result.publicationDate = fields.publicationDate;\n if (fields.volume)\n result.volume = fields.volume;\n if (fields.issue)\n result.issue = fields.issue;\n if (fields.pages)\n result.pages = fields.pages;\n if (fields.keywords.length > 0)\n result.keywords = fields.keywords;\n if (fields.articleType)\n result.articleType = fields.articleType;\n if (fields.license)\n result.license = fields.license;\n if (fields.abstract)\n result.abstract = fields.abstract;\n return result;\n}\n/**\n * Parse JATS XML front matter to extract article metadata.\n */\nexport function parseJatsMetadata(xml) {\n const parsed = parser.parse(xml);\n const article = findArticle(parsed);\n if (!article)\n return { title: \"\", authors: [] };\n const front = findChild(article.children, \"front\");\n if (!front)\n return { title: \"\", authors: [] };\n const articleMeta = findChild(front.children, \"article-meta\");\n if (!articleMeta)\n return { title: \"\", authors: [] };\n const metaChildren = articleMeta.children;\n const journal = parseJournalName(front.children);\n const publicationDate = parsePublicationDate(metaChildren);\n const articleType = article.attrs[\"article-type\"] || undefined;\n const license = parseLicense(metaChildren);\n const abstract = parseAbstract(metaChildren);\n return assembleMetadata({ title: parseArticleTitle(metaChildren), authors: parseAuthors(metaChildren) }, {\n ...parseArticleIds(metaChildren),\n ...(journal !== undefined ? { journal } : {}),\n ...(publicationDate !== undefined ? { publicationDate } : {}),\n ...parseVolumeAndPages(metaChildren),\n keywords: parseKeywords(metaChildren),\n ...(articleType !== undefined ? { articleType } : {}),\n ...(license !== undefined ? { license } : {}),\n ...(abstract !== undefined ? { abstract } : {}),\n });\n}\n// ─── Inline Content Parsing ──────────────────────────────────────────\n/** Handle <inline-formula> tag. */\nfunction handleInlineFormula(innerChildren) {\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 = {\n type: \"inline-formula\",\n text,\n };\n if (tex)\n entry.tex = tex;\n return entry;\n}\n/** Handle <ext-link> tag. */\nfunction handleExtLink(child, innerChildren) {\n const href = getAttr(child, \"xlink:href\");\n if (href) {\n return { type: \"link\", url: href, children: parseInlineContent(innerChildren) };\n }\n const linkText = extractAllText(innerChildren);\n if (linkText)\n return { type: \"text\", text: linkText };\n return null;\n}\n/** Handle <uri> tag. */\nfunction handleUri(child, innerChildren) {\n const href = getAttr(child, \"xlink:href\");\n const textContent = extractAllText(innerChildren);\n const url = href || textContent;\n if (url) {\n return { type: \"link\", url, children: parseInlineContent(innerChildren) };\n }\n return null;\n}\n/** Handle <xref> tag. */\nfunction handleXref(child, innerChildren) {\n const refType = getAttr(child, \"ref-type\");\n if (refType === \"bibr\") {\n return {\n type: \"citation\",\n refId: getAttr(child, \"rid\") ?? \"\",\n text: extractAllText(innerChildren),\n };\n }\n const xrefText = extractAllText(innerChildren);\n if (xrefText)\n return { type: \"text\", text: xrefText };\n return null;\n}\n/** Map of tag names to their inline content handlers. */\nconst inlineTagHandlers = {\n bold: (_child, innerChildren) => ({\n type: \"bold\",\n children: parseInlineContent(innerChildren),\n }),\n italic: (_child, innerChildren) => ({\n type: \"italic\",\n children: parseInlineContent(innerChildren),\n }),\n sup: (_child, innerChildren) => ({\n type: \"superscript\",\n text: extractAllText(innerChildren),\n }),\n sub: (_child, innerChildren) => ({\n type: \"subscript\",\n text: extractAllText(innerChildren),\n }),\n \"inline-formula\": (_child, innerChildren) => handleInlineFormula(innerChildren),\n monospace: (_child, innerChildren) => ({\n type: \"code\",\n text: extractAllText(innerChildren),\n }),\n \"ext-link\": (child, innerChildren) => handleExtLink(child, innerChildren),\n uri: (child, innerChildren) => handleUri(child, innerChildren),\n underline: (_child, innerChildren) => {\n const passText = extractAllText(innerChildren);\n return passText ? { type: \"text\", text: passText } : null;\n },\n sc: (_child, innerChildren) => {\n const passText = extractAllText(innerChildren);\n return passText ? { type: \"text\", text: passText } : null;\n },\n xref: (child, innerChildren) => handleXref(child, innerChildren),\n};\n/** Process a single inline child node into an InlineContent, or return null. */\nfunction processInlineChild(child) {\n // Text node\n const text = getTextContent(child);\n if (text != null) {\n return text ? { type: \"text\", text } : null;\n }\n const tag = getTagName(child);\n if (!tag)\n return null;\n const innerChildren = getChildren(child);\n const handler = inlineTagHandlers[tag];\n if (handler)\n return handler(child, innerChildren);\n // Unknown inline element -- extract text\n const unknownText = extractAllText(innerChildren);\n return unknownText ? { type: \"text\", text: unknownText } : null;\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) {\n const result = [];\n for (const child of children) {\n const content = processInlineChild(child);\n if (content)\n result.push(content);\n }\n return result;\n}\n// ─── Block Content Parsing ───────────────────────────────────────────\n/**\n * Parse a <list> element into a BlockElement.\n */\nfunction parseList(listNode) {\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 = [];\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 return { type: \"list\", ordered, items };\n}\n/**\n * Parse a table row into an array of cell text content.\n */\nfunction parseTableRow(trChildren) {\n const cells = [];\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(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 * Parse an already-parsed table-wrap node.\n */\nfunction parseTableWrap(tableWrapNode) {\n const children = getChildren(tableWrapNode);\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 const tableNode = findChild(children, \"table\");\n const result = {\n headers: [],\n rows: [],\n };\n if (captionStr)\n result.caption = captionStr;\n if (!tableNode)\n return result;\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 // 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 return result;\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) {\n const parsed = parser.parse(xml);\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 * Parse a <boxed-text> element into a boxed-text block.\n * Extracts optional title and recursively parses inner block content.\n */\nfunction parseBoxedText(node) {\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 = { type: \"boxed-text\", content };\n if (title)\n block.title = title;\n return block;\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) {\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 = [];\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 = { type: \"def-list\", items };\n if (title)\n block.title = title;\n return block;\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) {\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 // Try <alternatives> wrapper first\n const alternatives = findChild(children, \"alternatives\");\n const searchChildren = alternatives ? alternatives.children : children;\n const texMath = findChild(searchChildren, \"tex-math\");\n const block = { type: \"formula\" };\n if (id)\n block.id = id;\n if (label)\n block.label = label;\n if (texMath) {\n block.tex = extractAllText(texMath.children);\n }\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)\n block.text = text;\n }\n return block;\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 * Parse a <disp-quote> element into a blockquote block.\n * Extracts <p> children and concatenates their inline content.\n */\nfunction parseDispQuote(node) {\n const children = getChildren(node);\n const paragraphs = findChildren(children, \"p\");\n const content = [];\n for (let i = 0; i < paragraphs.length; i++) {\n if (i > 0)\n content.push({ type: \"text\", text: \"\\n\\n\" });\n const para = paragraphs[i];\n if (para)\n 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 * Parse a <table-wrap> node into a table block element.\n */\nfunction parseTableBlock(node) {\n const tableResult = parseTableWrap(node);\n const tableBlock = {\n type: \"table\",\n headers: tableResult.headers,\n rows: tableResult.rows,\n };\n if (tableResult.caption)\n tableBlock.caption = tableResult.caption;\n return tableBlock;\n}\n/**\n * Parse a <fig> node into a figure block element.\n */\nfunction parseFigBlock(node) {\n const innerChildren = getChildren(node);\n const figBlock = { type: \"figure\" };\n const figId = getAttr(node, \"id\");\n if (figId)\n figBlock.id = figId;\n const figLabel = findChild(innerChildren, \"label\");\n if (figLabel) {\n const labelText = extractAllText(figLabel.children);\n if (labelText)\n figBlock.label = labelText;\n }\n const figCaption = findChild(innerChildren, \"caption\");\n if (figCaption) {\n const captionText = extractAllText(figCaption.children);\n if (captionText)\n figBlock.caption = captionText;\n }\n return figBlock;\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) {\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 if (!hasNestedBlocks) {\n return [{ type: \"paragraph\", content: parseInlineContent(pChildren) }];\n }\n // Split into inline runs and block elements\n const blocks = [];\n let inlineBuffer = [];\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((c) => c.type !== \"text\" || c.text.trim() !== \"\");\n if (content.length > 0 && hasNonWhitespace) {\n blocks.push({ type: \"paragraph\", content });\n }\n inlineBuffer = [];\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 }\n else if (tag === \"fig\") {\n flushInline();\n blocks.push(parseFigBlock(child));\n }\n else if (tag === \"disp-quote\") {\n flushInline();\n blocks.push(parseDispQuote(child));\n }\n else if (tag === \"boxed-text\") {\n flushInline();\n blocks.push(parseBoxedText(child));\n }\n else {\n inlineBuffer.push(child);\n }\n }\n flushInline();\n return blocks;\n}\n/** Parse a <supplementary-material> element into a paragraph block. */\nfunction parseSupplementaryMaterial(child) {\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 return { type: \"paragraph\", content: [{ type: \"text\", text }] };\n }\n return null;\n}\n/** Map of tag names to their block content handlers. */\nconst blockTagHandlers = {\n p: (child) => parseParagraph(getChildren(child)),\n list: (child) => parseList(child),\n \"table-wrap\": (child) => parseTableBlock(child),\n fig: (child) => parseFigBlock(child),\n \"disp-quote\": (child) => parseDispQuote(child),\n \"boxed-text\": (child) => parseBoxedText(child),\n \"def-list\": (child) => parseDefList(child),\n \"disp-formula\": (child) => parseDispFormula(child),\n preformat: (child) => ({ type: \"preformat\", text: extractAllText(getChildren(child)) }),\n \"supplementary-material\": (child) => parseSupplementaryMaterial(child),\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) {\n const blocks = [];\n for (const child of sectionChildren) {\n const tag = getTagName(child);\n if (!tag)\n continue;\n const handler = blockTagHandlers[tag];\n if (!handler)\n continue;\n const result = handler(child);\n if (result == null)\n continue;\n if (Array.isArray(result)) {\n blocks.push(...result);\n }\n else {\n blocks.push(result);\n }\n }\n return blocks;\n}\n// ─── Section Parsing ─────────────────────────────────────────────────\n/**\n * Parse a <sec> element into a JatsSection, recursively handling subsections.\n */\nfunction parseSection(secChildren, level) {\n const titleNode = findChild(secChildren, \"title\");\n const title = titleNode ? extractAllText(titleNode.children) : \"\";\n const content = parseBlockContent(secChildren);\n // Nested sections\n const subsections = [];\n const nestedSecs = findChildren(secChildren, \"sec\");\n for (const sub of nestedSecs) {\n subsections.push(parseSection(sub.children, level + 1));\n }\n return { title, level, content, subsections };\n}\n/**\n * Parse JATS XML body to extract sections and content.\n */\nexport function parseJatsBody(xml) {\n const parsed = parser.parse(xml);\n const article = findArticle(parsed);\n if (!article)\n return [];\n const body = findChild(article.children, \"body\");\n if (!body)\n return [];\n const sections = [];\n const secs = findChildren(body.children, \"sec\");\n if (secs.length > 0) {\n for (const sec of secs) {\n sections.push(parseSection(sec.children, 2));\n }\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 return sections;\n}\n// ─── Reference Parsing ───────────────────────────────────────────────\n/** Extract authors from a <person-group> element. */\nfunction extractCitationAuthors(children) {\n const personGroup = findChild(children, \"person-group\");\n if (!personGroup)\n return undefined;\n const names = findChildren(personGroup.children, \"name\");\n const authorParts = [];\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} ${givenText}`);\n }\n else if (surnameText) {\n authorParts.push(surnameText);\n }\n }\n return authorParts.length > 0 ? authorParts.join(\", \") : undefined;\n}\n/** Format year, volume, and pages into a citation string part. */\nfunction formatYearVolumePage(children) {\n const year = findChild(children, \"year\");\n if (!year)\n return undefined;\n let yearStr = extractAllText(year.children);\n const volume = findChild(children, \"volume\");\n if (volume) {\n yearStr += `;${extractAllText(volume.children)}`;\n }\n const fpage = findChild(children, \"fpage\");\n if (fpage) {\n const fpageText = extractAllText(fpage.children);\n const lpage = findChild(children, \"lpage\");\n const lpageText = lpage ? extractAllText(lpage.children) : \"\";\n yearStr += `:${fpageText}${lpageText ? `-${lpageText}` : \"\"}`;\n }\n return yearStr;\n}\n/**\n * Format a structured <element-citation> into a readable reference string.\n * Produces: \"Author1, Author2. Title. Source. Year;Volume:FirstPage-LastPage.\"\n */\nfunction formatElementCitation(children) {\n const parts = [];\n const authorsStr = extractCitationAuthors(children);\n if (authorsStr)\n parts.push(authorsStr);\n // Article title\n const articleTitle = findChild(children, \"article-title\");\n if (articleTitle) {\n parts.push(extractAllText(articleTitle.children));\n }\n // Source (journal name)\n const source = findChild(children, \"source\");\n if (source) {\n parts.push(extractAllText(source.children));\n }\n // Year, volume, pages\n const yearVolumePage = formatYearVolumePage(children);\n if (yearVolumePage)\n parts.push(yearVolumePage);\n return `${parts.join(\". \")}.`;\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) {\n // Collect pub-id values\n const pubIds = findChildren(children, \"pub-id\");\n const pubIdValues = pubIds.map((p) => extractAllText(p.children).trim()).filter(Boolean);\n if (pubIdValues.length === 0) {\n return extractAllText(children).trim();\n }\n // Extract full text\n const fullText = extractAllText(children).trim();\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 return result;\n}\n/**\n * Extract structured pub-id values (DOI, PMID, PMCID) from children nodes.\n */\nfunction extractPubIds(children) {\n const pubIds = findChildren(children, \"pub-id\");\n const result = {};\n for (const p of pubIds) {\n const idType = p.attrs[\"pub-id-type\"];\n const value = extractAllText(p.children).trim();\n if (!value)\n continue;\n if (idType === \"doi\")\n result.doi = value;\n if (idType === \"pmid\")\n result.pmid = value;\n if (idType === \"pmc\" || idType === \"pmcid\") {\n result.pmcid = value.replace(/^PMC/, \"\");\n }\n }\n return result;\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(text, pubIds) {\n let result = text;\n const values = [pubIds.doi, pubIds.pmid, pubIds.pmcid].filter(Boolean);\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/** Parse a single <ref> element into a JatsReference, or return null if invalid. */\nfunction parseSingleReference(ref) {\n const id = getAttr(ref.node, \"id\") ?? \"\";\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 // 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)\n return { id, text, ...pubIds };\n return null;\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)\n return { id, text, ...pubIds };\n return null;\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 return { id, text };\n return null;\n}\n/**\n * Parse JATS XML back matter to extract references.\n */\nexport function parseJatsReferences(xml) {\n const parsed = parser.parse(xml);\n const article = findArticle(parsed);\n if (!article)\n return [];\n const back = findChild(article.children, \"back\");\n if (!back)\n return [];\n const refList = findChild(back.children, \"ref-list\");\n if (!refList)\n return [];\n const refs = findChildren(refList.children, \"ref\");\n const references = [];\n for (const ref of refs) {\n const reference = parseSingleReference(ref);\n if (reference)\n references.push(reference);\n }\n return references;\n}\n/** Parse acknowledgments from <ack> element. */\nfunction parseAcknowledgments(backChildren) {\n const ack = findChild(backChildren, \"ack\");\n if (!ack)\n return undefined;\n const paragraphs = findChildren(ack.children, \"p\");\n if (paragraphs.length > 0) {\n return paragraphs.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n }\n return undefined;\n}\n/** Parse appendices from <app-group>/<app> elements. */\nfunction parseAppendices(backChildren) {\n const appGroup = findChild(backChildren, \"app-group\");\n if (!appGroup)\n return undefined;\n const apps = findChildren(appGroup.children, \"app\");\n if (apps.length === 0)\n return undefined;\n return apps.map((app) => parseSection(app.children, 2));\n}\n/** Parse a single footnote element into a JatsFootnote. */\nfunction parseSingleFootnote(fn) {\n const parts = [];\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)\n 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)\n parts.push(pText);\n }\n return {\n id: getAttr(fn.node, \"id\") ?? \"\",\n text: parts.join(\" \"),\n };\n}\n/** Parse footnotes from <fn-group>/<fn> elements. */\nfunction parseFootnotes(backChildren) {\n const fnGroup = findChild(backChildren, \"fn-group\");\n if (!fnGroup)\n return undefined;\n const fns = findChildren(fnGroup.children, \"fn\");\n if (fns.length === 0)\n return undefined;\n return fns.map(parseSingleFootnote);\n}\n/** Parse a single notes element into BackMatterNote entries. */\nfunction parseSingleNotesElement(note) {\n const notes = [];\n // Check if this <notes> contains <sec> or nested <notes> children\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.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n if (subTitle || subText) {\n notes.push({ title: subTitle, text: subText });\n }\n }\n return notes;\n }\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.map((p) => extractAllText(p.children)).join(\"\\n\\n\");\n if (title || text) {\n notes.push({ title, text });\n }\n return notes;\n}\n/** Parse notes from <notes> elements (author contributions, funding, etc.). */\nfunction parseNotes(backChildren) {\n const notesElements = findChildren(backChildren, \"notes\");\n if (notesElements.length === 0)\n return undefined;\n const notes = [];\n for (const note of notesElements) {\n notes.push(...parseSingleNotesElement(note));\n }\n return notes.length > 0 ? notes : undefined;\n}\n/** Parse glossary elements into BackMatterNote entries. */\nfunction parseGlossary(backChildren) {\n const glossaryElements = findChildren(backChildren, \"glossary\");\n const notes = [];\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 continue;\n const defItems = findChildren(defList.children, \"def-item\");\n const lines = [];\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 notes.push({ title, text: lines.join(\"\\n\") });\n }\n return notes;\n}\n/** Parse <floats-group> into block elements. */\nfunction parseFloatsGroup(articleChildren) {\n const floatsGroup = findChild(articleChildren, \"floats-group\");\n if (!floatsGroup)\n return undefined;\n const blocks = [];\n for (const child of floatsGroup.children) {\n const tag = getTagName(child);\n if (tag === \"fig\") {\n blocks.push(parseFigBlock(child));\n }\n else if (tag === \"table-wrap\") {\n blocks.push(parseTableBlock(child));\n }\n }\n return blocks.length > 0 ? blocks : undefined;\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) {\n const parsed = parser.parse(xml);\n const article = findArticle(parsed);\n if (!article)\n return {};\n const result = {};\n // Parse <back> children\n const back = findChild(article.children, \"back\");\n if (back) {\n const ack = parseAcknowledgments(back.children);\n if (ack)\n result.acknowledgments = ack;\n const app = parseAppendices(back.children);\n if (app)\n result.appendices = app;\n const fn = parseFootnotes(back.children);\n if (fn)\n result.footnotes = fn;\n const notes = parseNotes(back.children);\n const glossaryNotes = parseGlossary(back.children);\n if (notes || glossaryNotes.length > 0) {\n result.notes = [...(notes ?? []), ...glossaryNotes];\n }\n }\n // Floats-group: <floats-group> (sibling of <body> and <back>)\n const floats = parseFloatsGroup(article.children);\n if (floats)\n result.floats = floats;\n return result;\n}\n//# 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package/dist/{fulltext → node_modules/@ncukondo/academic-fulltext/dist}/convert/markdown-writer.js RENAMED Viewed

@@ -1,5 +1,6 @@
 function formatAuthor(author) {
-  if (!author.givenNames) return author.surname;
+  if (!author.givenNames)
+    return author.surname;
   const initials = author.givenNames.split(/[\s.]+/).filter(Boolean).map((n) => n[0]).join("");
   return `${author.surname} ${initials}`;
 }
@@ -24,12 +25,71 @@ function renderInline(content) {
         return node.tex ? `$${node.tex}$` : node.text;
       case "link": {
         const linkText = renderInline(node.children);
-        if (linkText === node.url) return node.url;
+        if (linkText === node.url)
+          return node.url;
         return `[${linkText}](${node.url})`;
       }
     }
   }).join("");
 }
+function renderTable(block) {
+  const lines = [];
+  if (block.caption) {
+    lines.push(`*${block.caption}*`);
+    lines.push("");
+  }
+  if (block.headers.length > 0) {
+    lines.push(`| ${block.headers.join(" | ")} |`);
+    lines.push(`| ${block.headers.map(() => "---").join(" | ")} |`);
+  } else if (block.rows.length > 0) {
+    const colCount = block.rows[0]?.length ?? 0;
+    lines.push(`| ${Array.from({ length: colCount }, () => "").join(" | ")} |`);
+    lines.push(`| ${Array.from({ length: colCount }, () => "---").join(" | ")} |`);
+  }
+  for (const row of block.rows) {
+    lines.push(`| ${row.join(" | ")} |`);
+  }
+  return lines.join("\n");
+}
+function renderFormula(block) {
+  const lines = [];
+  if (block.tex) {
+    lines.push(`$$${block.tex}$$`);
+  } else if (block.text) {
+    lines.push("```");
+    lines.push(block.text);
+    lines.push("```");
+  }
+  if (block.label) {
+    lines.push(block.label);
+  }
+  return lines.join("\n");
+}
+function renderDefList(block) {
+  const lines = [];
+  if (block.title) {
+    lines.push(`**${block.title}**`);
+    lines.push("");
+  }
+  for (const item of block.items) {
+    lines.push(`**${item.term}**: ${item.definition}`);
+  }
+  return lines.join("\n");
+}
+function renderBoxedText(block) {
+  const lines = [];
+  if (block.title) {
+    lines.push(`> **${block.title}**`);
+    lines.push(">");
+  }
+  for (const inner of block.content) {
+    const rendered = renderBlock(inner);
+    for (const line of rendered.split("\n")) {
+      lines.push(line === "" ? ">" : `> ${line}`);
+    }
+  }
+  return lines.join("\n");
+}
 function renderBlock(block) {
   switch (block.type) {
     case "paragraph":
@@ -44,71 +104,23 @@ function renderBlock(block) {
         return `${prefix}${renderInline(item)}`;
       }).join("\n");
     }
-    case "table": {
-      const lines = [];
-      if (block.caption) {
-        lines.push(`*${block.caption}*`);
-        lines.push("");
-      }
-      if (block.headers.length > 0) {
-        lines.push(`| ${block.headers.join(" | ")} |`);
-        lines.push(`| ${block.headers.map(() => "---").join(" | ")} |`);
-      } else if (block.rows.length > 0) {
-        const colCount = block.rows[0].length;
-        lines.push(`| ${Array.from({ length: colCount }, () => "").join(" | ")} |`);
-        lines.push(`| ${Array.from({ length: colCount }, () => "---").join(" | ")} |`);
-      }
-      for (const row of block.rows) {
-        lines.push(`| ${row.join(" | ")} |`);
-      }
-      return lines.join("\n");
-    }
+    case "table":
+      return renderTable(block);
     case "figure": {
       const label = block.label ?? "Figure";
       const altText = block.caption ? `${label}. ${block.caption}` : label;
       return `![${altText}]()`;
     }
     case "preformat":
-      return "```\n" + block.text + "\n```";
-    case "formula": {
-      const lines = [];
-      if (block.tex) {
-        lines.push(`$$${block.tex}$$`);
-      } else if (block.text) {
-        lines.push("```");
-        lines.push(block.text);
-        lines.push("```");
-      }
-      if (block.label) {
-        lines.push(block.label);
-      }
-      return lines.join("\n");
-    }
-    case "def-list": {
-      const lines = [];
-      if (block.title) {
-        lines.push(`**${block.title}**`);
-        lines.push("");
-      }
-      for (const item of block.items) {
-        lines.push(`**${item.term}**: ${item.definition}`);
-      }
-      return lines.join("\n");
-    }
-    case "boxed-text": {
-      const lines = [];
-      if (block.title) {
-        lines.push(`> **${block.title}**`);
-        lines.push(">");
-      }
-      for (const inner of block.content) {
-        const rendered = renderBlock(inner);
-        rendered.split("\n").forEach((line) => {
-          lines.push(line === "" ? ">" : `> ${line}`);
-        });
-      }
-      return lines.join("\n");
-    }
+      return `\`\`\`
+${block.text}
+\`\`\``;
+    case "formula":
+      return renderFormula(block);
+    case "def-list":
+      return renderDefList(block);
+    case "boxed-text":
+      return renderBoxedText(block);
   }
 }
 function renderSection(section) {
@@ -141,7 +153,8 @@ function formatRefPubIds(ref) {
   return links.join(" ");
 }
 function renderReferences(references) {
-  if (references.length === 0) return "";
+  if (references.length === 0)
+    return "";
   const lines = ["## References", ""];
   references.forEach((ref, i) => {
     const pubIdLinks = formatRefPubIds(ref);
@@ -152,7 +165,8 @@ function renderReferences(references) {
   return lines.join("\n");
 }
 function renderFootnotes(footnotes) {
-  if (footnotes.length === 0) return "";
+  if (footnotes.length === 0)
+    return "";
   const lines = ["## Footnotes", ""];
   footnotes.forEach((fn, i) => {
     lines.push(`${i + 1}. ${fn.text}`);
@@ -161,7 +175,8 @@ function renderFootnotes(footnotes) {
   return lines.join("\n");
 }
 function renderFloats(floats) {
-  if (floats.length === 0) return "";
+  if (floats.length === 0)
+    return "";
   const lines = ["## Figures and Tables", ""];
   for (const block of floats) {
     lines.push(renderBlock(block));
@@ -169,71 +184,75 @@ function renderFloats(floats) {
   }
   return lines.join("\n");
 }
-function writeMarkdown(doc) {
+function formatPublicationDate(date) {
+  let dateStr = date.year;
+  if (date.month) {
+    dateStr += `-${date.month.padStart(2, "0")}`;
+    if (date.day)
+      dateStr += `-${date.day.padStart(2, "0")}`;
+  }
+  return dateStr;
+}
+function formatCitation(meta) {
+  if (meta.volume && meta.issue) {
+    let citation = `Vol. ${meta.volume}(${meta.issue})`;
+    if (meta.pages)
+      citation += `, pp. ${meta.pages}`;
+    return citation;
+  }
+  const parts = [];
+  if (meta.volume)
+    parts.push(`Vol. ${meta.volume}`);
+  if (meta.issue)
+    parts.push(`(${meta.issue})`);
+  if (meta.pages)
+    parts.push(`pp. ${meta.pages}`);
+  return parts.join(", ");
+}
+function renderMetadata(doc) {
   const lines = [];
-  lines.push(`# ${doc.metadata.title}`);
+  const meta = doc.metadata;
+  lines.push(`# ${meta.title}`);
   lines.push("");
-  if (doc.metadata.authors.length > 0) {
-    const authorStr = doc.metadata.authors.map(formatAuthor).join(", ");
+  const posAfterTitle = lines.length;
+  if (meta.authors.length > 0) {
+    const authorStr = meta.authors.map(formatAuthor).join(", ");
     lines.push(`**Authors**: ${authorStr}`);
   }
-  if (doc.metadata.doi) {
-    lines.push(`**DOI**: ${doc.metadata.doi}`);
-  }
-  if (doc.metadata.pmcid) {
-    lines.push(`**PMC**: PMC${doc.metadata.pmcid}`);
-  }
-  if (doc.metadata.pmid) {
-    lines.push(`**PMID**: ${doc.metadata.pmid}`);
-  }
-  if (doc.metadata.journal) {
-    lines.push(`**Journal**: ${doc.metadata.journal}`);
+  if (meta.doi)
+    lines.push(`**DOI**: ${meta.doi}`);
+  if (meta.pmcid)
+    lines.push(`**PMC**: PMC${meta.pmcid}`);
+  if (meta.pmid)
+    lines.push(`**PMID**: ${meta.pmid}`);
+  if (meta.journal)
+    lines.push(`**Journal**: ${meta.journal}`);
+  if (meta.publicationDate) {
+    lines.push(`**Published**: ${formatPublicationDate(meta.publicationDate)}`);
   }
-  if (doc.metadata.publicationDate) {
-    const d = doc.metadata.publicationDate;
-    let dateStr = d.year;
-    if (d.month) {
-      dateStr += `-${d.month.padStart(2, "0")}`;
-      if (d.day) dateStr += `-${d.day.padStart(2, "0")}`;
-    }
-    lines.push(`**Published**: ${dateStr}`);
-  }
-  if (doc.metadata.volume || doc.metadata.issue || doc.metadata.pages) {
-    const parts = [];
-    if (doc.metadata.volume) parts.push(`Vol. ${doc.metadata.volume}`);
-    if (doc.metadata.issue) parts.push(`(${doc.metadata.issue})`);
-    if (doc.metadata.pages) parts.push(`pp. ${doc.metadata.pages}`);
-    let citation = "";
-    if (doc.metadata.volume && doc.metadata.issue) {
-      citation = `Vol. ${doc.metadata.volume}(${doc.metadata.issue})`;
-      if (doc.metadata.pages) citation += `, pp. ${doc.metadata.pages}`;
-    } else {
-      citation = parts.join(", ");
-    }
-    lines.push(`**Citation**: ${citation}`);
-  }
-  if (doc.metadata.articleType) {
-    lines.push(`**Article Type**: ${doc.metadata.articleType}`);
-  }
-  if (doc.metadata.keywords && doc.metadata.keywords.length > 0) {
-    lines.push(`**Keywords**: ${doc.metadata.keywords.join(", ")}`);
+  if (meta.volume || meta.issue || meta.pages) {
+    lines.push(`**Citation**: ${formatCitation(meta)}`);
   }
-  if (doc.metadata.license) {
-    lines.push(`**License**: ${doc.metadata.license}`);
+  if (meta.articleType)
+    lines.push(`**Article Type**: ${meta.articleType}`);
+  if (meta.keywords && meta.keywords.length > 0) {
+    lines.push(`**Keywords**: ${meta.keywords.join(", ")}`);
   }
-  const hasMetaLines = doc.metadata.authors.length > 0 || doc.metadata.doi || doc.metadata.pmcid || doc.metadata.pmid || doc.metadata.journal || doc.metadata.publicationDate || doc.metadata.volume || doc.metadata.pages || doc.metadata.keywords && doc.metadata.keywords.length > 0 || doc.metadata.articleType || doc.metadata.license;
-  if (hasMetaLines) {
+  if (meta.license)
+    lines.push(`**License**: ${meta.license}`);
+  if (lines.length > posAfterTitle) {
     lines.push("");
   }
-  if (doc.metadata.abstract) {
+  if (meta.abstract) {
     lines.push("## Abstract");
     lines.push("");
-    lines.push(doc.metadata.abstract);
+    lines.push(meta.abstract);
     lines.push("");
   }
-  for (const section of doc.sections) {
-    lines.push(renderSection(section));
-  }
+  return lines;
+}
+function renderTrailingSections(doc) {
+  const lines = [];
   if (doc.acknowledgments) {
     lines.push("## Acknowledgments");
     lines.push("");
@@ -262,7 +281,17 @@ function writeMarkdown(doc) {
   if (doc.floats && doc.floats.length > 0) {
     lines.push(renderFloats(doc.floats));
   }
-  return lines.join("\n").trimEnd() + "\n";
+  return lines;
+}
+function writeMarkdown(doc) {
+  const lines = [];
+  lines.push(...renderMetadata(doc));
+  for (const section of doc.sections) {
+    lines.push(renderSection(section));
+  }
+  lines.push(...renderTrailingSections(doc));
+  return `${lines.join("\n").trimEnd()}
+`;
 }
 export {
   writeMarkdown

package/dist/node_modules/@ncukondo/academic-fulltext/dist/convert/markdown-writer.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"markdown-writer.js","sources":["../../../../../../node_modules/@ncukondo/academic-fulltext/dist/convert/markdown-writer.js"],"sourcesContent":["/**\n * Markdown writer for JATS XML conversion.\n *\n * Converts the intermediate JatsDocument representation to Markdown text.\n */\n/**\n * Format an author's name in abbreviated form (e.g., \"Smith J\").\n */\nfunction formatAuthor(author) {\n if (!author.givenNames)\n return author.surname;\n const initials = author.givenNames\n .split(/[\\s.]+/)\n .filter(Boolean)\n .map((n) => n[0])\n .join(\"\");\n return `${author.surname} ${initials}`;\n}\n/**\n * Render inline content to Markdown string.\n */\nfunction renderInline(content) {\n return content\n .map((node) => {\n switch (node.type) {\n case \"text\":\n return node.text;\n case \"bold\":\n return `**${renderInline(node.children)}**`;\n case \"italic\":\n return `*${renderInline(node.children)}*`;\n case \"superscript\":\n return `^${node.text}^`;\n case \"subscript\":\n return `~${node.text}~`;\n case \"citation\":\n return node.text;\n case \"code\":\n return `\\`${node.text}\\``;\n case \"inline-formula\":\n return node.tex ? `$${node.tex}$` : node.text;\n case \"link\": {\n const linkText = renderInline(node.children);\n if (linkText === node.url)\n return node.url;\n return `[${linkText}](${node.url})`;\n }\n }\n })\n .join(\"\");\n}\n/**\n * Render a table block to Markdown.\n */\nfunction renderTable(block) {\n const lines = [];\n if (block.caption) {\n lines.push(`*${block.caption}*`);\n lines.push(\"\");\n }\n if (block.headers.length > 0) {\n lines.push(`| ${block.headers.join(\" | \")} |`);\n lines.push(`| ${block.headers.map(() => \"---\").join(\" | \")} |`);\n }\n else if (block.rows.length > 0) {\n const colCount = block.rows[0]?.length ?? 0;\n lines.push(`| ${Array.from({ length: colCount }, () => \"\").join(\" | \")} |`);\n lines.push(`| ${Array.from({ length: colCount }, () => \"---\").join(\" | \")} |`);\n }\n for (const row of block.rows) {\n lines.push(`| ${row.join(\" | \")} |`);\n }\n return lines.join(\"\\n\");\n}\n/**\n * Render a formula block to Markdown.\n */\nfunction renderFormula(block) {\n const lines = [];\n if (block.tex) {\n lines.push(`$$${block.tex}$$`);\n }\n else if (block.text) {\n lines.push(\"```\");\n lines.push(block.text);\n lines.push(\"```\");\n }\n if (block.label) {\n lines.push(block.label);\n }\n return lines.join(\"\\n\");\n}\n/**\n * Render a definition list block to Markdown.\n */\nfunction renderDefList(block) {\n const lines = [];\n if (block.title) {\n lines.push(`**${block.title}**`);\n lines.push(\"\");\n }\n for (const item of block.items) {\n lines.push(`**${item.term}**: ${item.definition}`);\n }\n return lines.join(\"\\n\");\n}\n/**\n * Render a boxed-text block to Markdown.\n */\nfunction renderBoxedText(block) {\n const lines = [];\n if (block.title) {\n lines.push(`> **${block.title}**`);\n lines.push(\">\");\n }\n for (const inner of block.content) {\n const rendered = renderBlock(inner);\n for (const line of rendered.split(\"\\n\")) {\n lines.push(line === \"\" ? \">\" : `> ${line}`);\n }\n }\n return lines.join(\"\\n\");\n}\n/**\n * Render a block element to Markdown lines.\n */\nfunction renderBlock(block) {\n switch (block.type) {\n case \"paragraph\":\n return renderInline(block.content);\n case \"blockquote\": {\n const text = renderInline(block.content);\n return text\n .split(\"\\n\")\n .map((line) => (line === \"\" ? \">\" : `> ${line}`))\n .join(\"\\n\");\n }\n case \"list\": {\n return block.items\n .map((item, i) => {\n const prefix = block.ordered ? `${i + 1}. ` : \"- \";\n return `${prefix}${renderInline(item)}`;\n })\n .join(\"\\n\");\n }\n case \"table\":\n return renderTable(block);\n case \"figure\": {\n const label = block.label ?? \"Figure\";\n const altText = block.caption ? `${label}. ${block.caption}` : label;\n return `![${altText}]()`;\n }\n case \"preformat\":\n return `\\`\\`\\`\\n${block.text}\\n\\`\\`\\``;\n case \"formula\":\n return renderFormula(block);\n case \"def-list\":\n return renderDefList(block);\n case \"boxed-text\":\n return renderBoxedText(block);\n }\n}\n/**\n * Render a section and its subsections to Markdown.\n */\nfunction renderSection(section) {\n const lines = [];\n const heading = \"#\".repeat(section.level);\n if (section.title.trim()) {\n lines.push(`${heading} ${section.title}`);\n lines.push(\"\");\n }\n for (const block of section.content) {\n lines.push(renderBlock(block));\n lines.push(\"\");\n }\n for (const sub of section.subsections) {\n lines.push(renderSection(sub));\n }\n return lines.join(\"\\n\");\n}\n/**\n * Render references section.\n */\nfunction formatRefPubIds(ref) {\n const links = [];\n if (ref.doi) {\n links.push(`[doi:${ref.doi}](https://doi.org/${ref.doi})`);\n }\n if (ref.pmid) {\n links.push(`[pmid:${ref.pmid}](https://pubmed.ncbi.nlm.nih.gov/${ref.pmid}/)`);\n }\n if (ref.pmcid) {\n links.push(`[pmcid:PMC${ref.pmcid}](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC${ref.pmcid}/)`);\n }\n return links.join(\" \");\n}\nfunction renderReferences(references) {\n if (references.length === 0)\n return \"\";\n const lines = [\"## References\", \"\"];\n references.forEach((ref, i) => {\n const pubIdLinks = formatRefPubIds(ref);\n const line = pubIdLinks ? `${i + 1}. ${ref.text} ${pubIdLinks}` : `${i + 1}. ${ref.text}`;\n lines.push(line);\n });\n lines.push(\"\");\n return lines.join(\"\\n\");\n}\n/**\n * Render footnotes section.\n */\nfunction renderFootnotes(footnotes) {\n if (footnotes.length === 0)\n return \"\";\n const lines = [\"## Footnotes\", \"\"];\n footnotes.forEach((fn, i) => {\n lines.push(`${i + 1}. ${fn.text}`);\n });\n lines.push(\"\");\n return lines.join(\"\\n\");\n}\n/**\n * Render floats (figures and tables) section.\n */\nfunction renderFloats(floats) {\n if (floats.length === 0)\n return \"\";\n const lines = [\"## Figures and Tables\", \"\"];\n for (const block of floats) {\n lines.push(renderBlock(block));\n lines.push(\"\");\n }\n return lines.join(\"\\n\");\n}\n/**\n * Format a publication date as a string (e.g., \"2024\", \"2024-01\", \"2024-01-15\").\n */\nfunction formatPublicationDate(date) {\n let dateStr = date.year;\n if (date.month) {\n dateStr += `-${date.month.padStart(2, \"0\")}`;\n if (date.day)\n dateStr += `-${date.day.padStart(2, \"0\")}`;\n }\n return dateStr;\n}\n/**\n * Format a citation string from volume, issue, and pages.\n */\nfunction formatCitation(meta) {\n if (meta.volume && meta.issue) {\n let citation = `Vol. ${meta.volume}(${meta.issue})`;\n if (meta.pages)\n citation += `, pp. ${meta.pages}`;\n return citation;\n }\n const parts = [];\n if (meta.volume)\n parts.push(`Vol. ${meta.volume}`);\n if (meta.issue)\n parts.push(`(${meta.issue})`);\n if (meta.pages)\n parts.push(`pp. ${meta.pages}`);\n return parts.join(\", \");\n}\n/**\n * Render document metadata (authors, DOI, journal, etc.) to Markdown lines.\n */\nfunction renderMetadata(doc) {\n const lines = [];\n const meta = doc.metadata;\n // Title\n lines.push(`# ${meta.title}`);\n lines.push(\"\");\n // Track position after title to detect if any metadata fields were added\n const posAfterTitle = lines.length;\n // Authors\n if (meta.authors.length > 0) {\n const authorStr = meta.authors.map(formatAuthor).join(\", \");\n lines.push(`**Authors**: ${authorStr}`);\n }\n if (meta.doi)\n lines.push(`**DOI**: ${meta.doi}`);\n if (meta.pmcid)\n lines.push(`**PMC**: PMC${meta.pmcid}`);\n if (meta.pmid)\n lines.push(`**PMID**: ${meta.pmid}`);\n if (meta.journal)\n lines.push(`**Journal**: ${meta.journal}`);\n if (meta.publicationDate) {\n lines.push(`**Published**: ${formatPublicationDate(meta.publicationDate)}`);\n }\n if (meta.volume || meta.issue || meta.pages) {\n lines.push(`**Citation**: ${formatCitation(meta)}`);\n }\n if (meta.articleType)\n lines.push(`**Article Type**: ${meta.articleType}`);\n if (meta.keywords && meta.keywords.length > 0) {\n lines.push(`**Keywords**: ${meta.keywords.join(\", \")}`);\n }\n if (meta.license)\n lines.push(`**License**: ${meta.license}`);\n if (lines.length > posAfterTitle) {\n lines.push(\"\");\n }\n // Abstract\n if (meta.abstract) {\n lines.push(\"## Abstract\");\n lines.push(\"\");\n lines.push(meta.abstract);\n lines.push(\"\");\n }\n return lines;\n}\n/**\n * Render trailing sections (acknowledgments, notes, references, appendices,\n * footnotes, floats) to Markdown lines.\n */\nfunction renderTrailingSections(doc) {\n const lines = [];\n // Acknowledgments (before References)\n if (doc.acknowledgments) {\n lines.push(\"## Acknowledgments\");\n lines.push(\"\");\n lines.push(doc.acknowledgments);\n lines.push(\"\");\n }\n // Notes (between Acknowledgments and References)\n if (doc.notes && doc.notes.length > 0) {\n for (const note of doc.notes) {\n lines.push(`## ${note.title}`);\n lines.push(\"\");\n lines.push(note.text);\n lines.push(\"\");\n }\n }\n // References\n if (doc.references.length > 0) {\n lines.push(renderReferences(doc.references));\n }\n // Appendices (after References)\n if (doc.appendices && doc.appendices.length > 0) {\n for (const appendix of doc.appendices) {\n lines.push(renderSection(appendix));\n }\n }\n // Footnotes\n if (doc.footnotes && doc.footnotes.length > 0) {\n lines.push(renderFootnotes(doc.footnotes));\n }\n // Floats (Figures and Tables from floats-group)\n if (doc.floats && doc.floats.length > 0) {\n lines.push(renderFloats(doc.floats));\n }\n return lines;\n}\n/**\n * Convert a parsed JATS document to Markdown string.\n */\nexport function writeMarkdown(doc) {\n const lines = [];\n lines.push(...renderMetadata(doc));\n // Sections\n for (const section of doc.sections) {\n lines.push(renderSection(section));\n }\n lines.push(...renderTrailingSections(doc));\n return `${lines.join(\"\\n\").trimEnd()}\\n`;\n}\n//# 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package/dist/{fulltext → node_modules/@ncukondo/academic-fulltext/dist}/discovery/arxiv.js RENAMED Viewed

@@ -2,7 +2,8 @@ function normalizeArxivId(id) {
   return id.replace(/^arXiv:/i, "");
 }
 function checkArxiv(arxivId) {
-  if (!arxivId) return null;
+  if (!arxivId)
+    return null;
   const id = normalizeArxivId(arxivId);
   return [
     {
@@ -10,6 +11,12 @@ function checkArxiv(arxivId) {
       url: `https://arxiv.org/pdf/${id}.pdf`,
       urlType: "pdf",
       version: "submitted"
+    },
+    {
+      source: "arxiv",
+      url: `https://arxiv.org/html/${id}`,
+      urlType: "html",
+      version: "submitted"
     }
   ];
 }

package/dist/node_modules/@ncukondo/academic-fulltext/dist/discovery/arxiv.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"arxiv.js","sources":["../../../../../../node_modules/@ncukondo/academic-fulltext/dist/discovery/arxiv.js"],"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/** Strip common prefixes from arXiv IDs */\nfunction normalizeArxivId(id) {\n return id.replace(/^arXiv:/i, \"\");\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) {\n if (!arxivId)\n return null;\n const id = normalizeArxivId(arxivId);\n return [\n {\n source: \"arxiv\",\n url: `https://arxiv.org/pdf/${id}.pdf`,\n urlType: \"pdf\",\n version: \"submitted\",\n },\n {\n source: \"arxiv\",\n url: `https://arxiv.org/html/${id}`,\n urlType: \"html\",\n version: \"submitted\",\n },\n ];\n}\n//# sourceMappingURL=arxiv.js.map"],"names":[],"mappings":"AAQA,SAAS,iBAAiB,IAAI;AAC1B,SAAO,GAAG,QAAQ,YAAY,EAAE;AACpC;AASO,SAAS,WAAW,SAAS;AAChC,MAAI,CAAC;AACD,WAAO;AACX,QAAM,KAAK,iBAAiB,OAAO;AACnC,SAAO;AAAA,IACH;AAAA,MACI,QAAQ;AAAA,MACR,KAAK,yBAAyB,EAAE;AAAA,MAChC,SAAS;AAAA,MACT,SAAS;AAAA,IACrB;AAAA,IACQ;AAAA,MACI,QAAQ;AAAA,MACR,KAAK,0BAA0B,EAAE;AAAA,MACjC,SAAS;AAAA,MACT,SAAS;AAAA,IACrB;AAAA,EACA;AACA;","x_google_ignoreList":[0]}

package/dist/{fulltext → node_modules/@ncukondo/academic-fulltext/dist}/discovery/core.js RENAMED Viewed

@@ -1,7 +1,9 @@
 const CORE_API_BASE = "https://api.core.ac.uk/v3";
 async function checkCore(doi, apiKey) {
-  if (!doi) return null;
-  if (!apiKey) return null;
+  if (!doi)
+    return null;
+  if (!apiKey)
+    return null;
   const url = `${CORE_API_BASE}/search/works?q=doi:"${doi}"&limit=1`;
   const response = await fetch(url, {
     headers: {
@@ -19,7 +21,8 @@ async function checkCore(doi, apiKey) {
     return null;
   }
   const firstResult = data.results[0];
-  if (!firstResult) return null;
+  if (!firstResult)
+    return null;
   if (firstResult.downloadUrl) {
     return [
       {

package/dist/node_modules/@ncukondo/academic-fulltext/dist/discovery/core.js.map ADDED Viewed

@@ -0,0 +1 @@

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