@ncukondo/search-hub 0.12.1 → 0.13.0

package/dist/cli/commands/diff.js.map

@@ -1 +1 @@
-{"version":3,"file":"diff.js","sources":["../../../src/cli/commands/diff.ts"],"sourcesContent":["import type { Article } from '../../providers/base/types.js';\nimport type { QueryAST, FieldType, TermBlock } from '../../query/types.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport interface DiffResult {\n  session1Count: number;\n  session2Count: number;\n  added: Article[];\n  removed: Article[];\n  common: Article[];\n}\n\n/**\n * Compute the diff between two sets of articles.\n *\n * Articles are matched by identifiers (DOI, PMID, arXiv ID, Scopus ID, ERIC ID).\n * Two articles are considered the same if they share any identifier.\n * Articles without identifiers cannot be matched.\n */\nexport function computeDiff(session1: Article[], session2: Article[]): DiffResult {\n  // Build a set of all identifier keys from session1\n  const session1Keys = new Set<string>();\n  for (const article of session1) {\n    for (const key of getArticleKeys(article)) {\n      session1Keys.add(key);\n    }\n  }\n\n  // Build a set of all identifier keys from session2\n  const session2Keys = new Set<string>();\n  for (const article of session2) {\n    for (const key of getArticleKeys(article)) {\n      session2Keys.add(key);\n    }\n  }\n\n  // Classify session1 articles as common or removed\n  const common: Article[] = [];\n  const removed: Article[] = [];\n  for (const article of session1) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as removed\n      removed.push(article);\n      continue;\n    }\n    const isInSession2 = keys.some((key) => session2Keys.has(key));\n    if (isInSession2) {\n      common.push(article);\n    } else {\n      removed.push(article);\n    }\n  }\n\n  // Classify session2 articles as added (those not in session1)\n  const added: Article[] = [];\n  for (const article of session2) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as added\n      added.push(article);\n      continue;\n    }\n    const isInSession1 = keys.some((key) => session1Keys.has(key));\n    if (!isInSession1) {\n      added.push(article);\n    }\n  }\n\n  return {\n    session1Count: session1.length,\n    session2Count: session2.length,\n    added,\n    removed,\n    common,\n  };\n}\n\nexport type ShowFilter = 'added' | 'removed' | 'common';\n\n/**\n * Extract a year string from publicationDate, or return empty string.\n */\nfunction extractYear(publicationDate: string | undefined): string {\n  if (!publicationDate) return '';\n  const year = publicationDate.substring(0, 4);\n  return /^\\d{4}$/.test(year) ? year : '';\n}\n\n/**\n * Format an article line for display.\n */\nfunction formatArticleLine(prefix: string, article: Article): string {\n  const year = extractYear(article.publicationDate);\n  const yearPart = year ? `[${year}] ` : '';\n  return `  ${prefix} ${yearPart}${article.title}`;\n}\n\n/**\n * Options for formatting diff with query information.\n */\nexport interface FormatDiffOptions {\n  queryDiff?: QueryDiff | undefined;\n  noQueryDiff?: boolean | undefined;\n  showQueryDiffPlaceholder?: boolean | undefined;\n}\n\n/**\n * Format diff result as human-readable text.\n */\nexport function formatDiff(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n  options?: FormatDiffOptions,\n): string {\n  const lines: string[] = [];\n\n  // Header\n  lines.push(`Diff: ${session1Id} → ${session2Id}`);\n  lines.push(`  Session 1: ${diff.session1Count} articles (${session1Id})`);\n  lines.push(`  Session 2: ${diff.session2Count} articles (${session2Id})`);\n  lines.push('');\n\n  // Query changes section (if available and not disabled)\n  const shouldShowQueryDiff = options?.queryDiff && !options?.noQueryDiff;\n  const shouldShowPlaceholder = options?.showQueryDiffPlaceholder && !options?.queryDiff && !options?.noQueryDiff;\n\n  if (shouldShowPlaceholder) {\n    lines.push('Query changes: (query data not available)');\n    lines.push('');\n  } else if (shouldShowQueryDiff) {\n    lines.push(formatQueryDiff(options.queryDiff!));\n    lines.push('');\n    lines.push('Result changes:');\n  }\n\n  // Summary counts\n  lines.push(`  Common:  ${diff.common.length} articles`);\n  lines.push(`  Added:   ${diff.added.length} articles (in ${session2Id} but not ${session1Id})`);\n  lines.push(`  Removed: ${diff.removed.length} articles (in ${session1Id} but not ${session2Id})`);\n\n  // Article lists based on show filter\n  const showAdded = !show || show === 'added';\n  const showRemoved = !show || show === 'removed';\n  const showCommon = show === 'common';\n\n  if (showAdded && diff.added.length > 0) {\n    lines.push('');\n    lines.push(`Added (+${diff.added.length}):`);\n    for (const article of diff.added) {\n      lines.push(formatArticleLine('+', article));\n    }\n  }\n\n  if (showRemoved && diff.removed.length > 0) {\n    lines.push('');\n    lines.push(`Removed (-${diff.removed.length}):`);\n    for (const article of diff.removed) {\n      lines.push(formatArticleLine('-', article));\n    }\n  }\n\n  if (showCommon && diff.common.length > 0) {\n    lines.push('');\n    lines.push(`Common (${diff.common.length}):`);\n    for (const article of diff.common) {\n      lines.push(formatArticleLine('=', article));\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format diff result as JSON.\n */\ninterface DiffJsonOutput {\n  session1: string;\n  session2: string;\n  summary: {\n    session1Count: number;\n    session2Count: number;\n    commonCount: number;\n    addedCount: number;\n    removedCount: number;\n  };\n  queryDiff?: QueryDiff;\n  added?: Article[];\n  removed?: Article[];\n  common?: Article[];\n}\n\nexport function formatDiffJson(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n  options?: FormatDiffOptions,\n): string {\n  const result: DiffJsonOutput = {\n    session1: session1Id,\n    session2: session2Id,\n    summary: {\n      session1Count: diff.session1Count,\n      session2Count: diff.session2Count,\n      commonCount: diff.common.length,\n      addedCount: diff.added.length,\n      removedCount: diff.removed.length,\n    },\n  };\n\n  // Add queryDiff if available and not disabled\n  if (options?.queryDiff && !options?.noQueryDiff) {\n    result.queryDiff = options.queryDiff;\n  }\n\n  if (!show || show === 'added') {\n    result.added = diff.added;\n  }\n  if (!show || show === 'removed') {\n    result.removed = diff.removed;\n  }\n  if (!show || show === 'common') {\n    result.common = diff.common;\n  }\n\n  return JSON.stringify(result, null, 2);\n}\n\n/**\n * Diff result for a single query block.\n */\nexport interface BlockDiff {\n  index: number;\n  field: FieldType;\n  added: string[];\n  removed: string[];\n  meshAdded?: string[];\n  meshRemoved?: string[];\n  emtreeAdded?: string[];\n  emtreeRemoved?: string[];\n  excludeAdded?: string[];\n  excludeRemoved?: string[];\n  hasChanges: boolean;\n  isNew?: boolean;\n  isRemoved?: boolean;\n}\n\n/**\n * Diff result for query filters.\n */\nexport interface FilterDiff {\n  yearFromChanged: boolean;\n  oldYearFrom?: number | undefined;\n  newYearFrom?: number | undefined;\n  yearToChanged: boolean;\n  oldYearTo?: number | undefined;\n  newYearTo?: number | undefined;\n  languagesAdded: string[];\n  languagesRemoved: string[];\n}\n\n/**\n * Complete query diff result.\n */\nexport interface QueryDiff {\n  blocks: BlockDiff[];\n  filters: FilterDiff;\n}\n\n/**\n * Compute the set difference: elements in arr2 not in arr1.\n */\nfunction setDiff(arr1: string[], arr2: string[]): string[] {\n  const set1 = new Set(arr1);\n  return arr2.filter((item) => !set1.has(item));\n}\n\n/**\n * Compare two query blocks and return the differences.\n */\nfunction compareBlocks(\n  block1: TermBlock | undefined,\n  block2: TermBlock | undefined,\n  index: number,\n  field: FieldType,\n): BlockDiff {\n  const emptyTerms = { keywords: [] as string[], mesh: [] as string[], emtree: [] as string[], exclude: [] as string[] };\n  const terms1 = block1 ?? emptyTerms;\n  const terms2 = block2 ?? emptyTerms;\n\n  const added = setDiff(terms1.keywords, terms2.keywords);\n  const removed = setDiff(terms2.keywords, terms1.keywords);\n  const meshAdded = setDiff(terms1.mesh ?? [], terms2.mesh ?? []);\n  const meshRemoved = setDiff(terms2.mesh ?? [], terms1.mesh ?? []);\n  const emtreeAdded = setDiff(terms1.emtree ?? [], terms2.emtree ?? []);\n  const emtreeRemoved = setDiff(terms2.emtree ?? [], terms1.emtree ?? []);\n  const excludeAdded = setDiff(terms1.exclude ?? [], terms2.exclude ?? []);\n  const excludeRemoved = setDiff(terms2.exclude ?? [], terms1.exclude ?? []);\n\n  const hasChanges =\n    added.length > 0 ||\n    removed.length > 0 ||\n    meshAdded.length > 0 ||\n    meshRemoved.length > 0 ||\n    emtreeAdded.length > 0 ||\n    emtreeRemoved.length > 0 ||\n    excludeAdded.length > 0 ||\n    excludeRemoved.length > 0;\n\n  const result: BlockDiff = {\n    index,\n    field,\n    added,\n    removed,\n    hasChanges,\n  };\n\n  if (meshAdded.length > 0 || meshRemoved.length > 0) {\n    result.meshAdded = meshAdded;\n    result.meshRemoved = meshRemoved;\n  }\n  if (emtreeAdded.length > 0 || emtreeRemoved.length > 0) {\n    result.emtreeAdded = emtreeAdded;\n    result.emtreeRemoved = emtreeRemoved;\n  }\n  if (excludeAdded.length > 0 || excludeRemoved.length > 0) {\n    result.excludeAdded = excludeAdded;\n    result.excludeRemoved = excludeRemoved;\n  }\n\n  if (!block1) {\n    result.isNew = true;\n    result.hasChanges = true;\n  }\n  if (!block2) {\n    result.isRemoved = true;\n    result.hasChanges = true;\n  }\n\n  return result;\n}\n\n/**\n * Compute the diff between two QueryAST objects.\n */\nexport function computeQueryDiff(query1: QueryAST, query2: QueryAST): QueryDiff {\n  const blocks: BlockDiff[] = [];\n\n  const maxBlocks = Math.max(query1.blocks.length, query2.blocks.length);\n\n  for (let i = 0; i < maxBlocks; i++) {\n    const block1 = query1.blocks[i];\n    const block2 = query2.blocks[i];\n\n    const field = block2?.field ?? block1?.field ?? 'all';\n    const blockDiff = compareBlocks(\n      block1?.terms,\n      block2?.terms,\n      i,\n      field,\n    );\n    blocks.push(blockDiff);\n  }\n\n  // Compare filters\n  const filters: FilterDiff = {\n    yearFromChanged: query1.filters.yearFrom !== query2.filters.yearFrom,\n    yearToChanged: query1.filters.yearTo !== query2.filters.yearTo,\n    languagesAdded: setDiff(query1.filters.languages ?? [], query2.filters.languages ?? []),\n    languagesRemoved: setDiff(query2.filters.languages ?? [], query1.filters.languages ?? []),\n  };\n\n  if (filters.yearFromChanged) {\n    filters.oldYearFrom = query1.filters.yearFrom;\n    filters.newYearFrom = query2.filters.yearFrom;\n  }\n  if (filters.yearToChanged) {\n    filters.oldYearTo = query1.filters.yearTo;\n    filters.newYearTo = query2.filters.yearTo;\n  }\n\n  return { blocks, filters };\n}\n\n/**\n * Format query diff as human-readable text.\n */\nexport function formatQueryDiff(queryDiff: QueryDiff): string {\n  const lines: string[] = [];\n\n  lines.push('Query changes:');\n\n  // Format block changes\n  for (const block of queryDiff.blocks) {\n    const blockNum = block.index + 1;\n    let blockHeader = `  Block ${blockNum} (${block.field})`;\n    if (block.isNew) {\n      blockHeader += ' (new block)';\n    } else if (block.isRemoved) {\n      blockHeader += ' (removed block)';\n    }\n\n    if (!block.hasChanges) {\n      lines.push(`${blockHeader}: no changes`);\n    } else {\n      lines.push(`${blockHeader}:`);\n\n      // Added keywords\n      for (const keyword of block.added) {\n        lines.push(`    + ${keyword}`);\n      }\n\n      // Removed keywords\n      for (const keyword of block.removed) {\n        lines.push(`    - ${keyword}`);\n      }\n\n      // MeSH changes\n      if (block.meshAdded) {\n        for (const term of block.meshAdded) {\n          lines.push(`    + [MeSH] ${term}`);\n        }\n      }\n      if (block.meshRemoved) {\n        for (const term of block.meshRemoved) {\n          lines.push(`    - [MeSH] ${term}`);\n        }\n      }\n\n      // Emtree changes\n      if (block.emtreeAdded) {\n        for (const term of block.emtreeAdded) {\n          lines.push(`    + [Emtree] ${term}`);\n        }\n      }\n      if (block.emtreeRemoved) {\n        for (const term of block.emtreeRemoved) {\n          lines.push(`    - [Emtree] ${term}`);\n        }\n      }\n\n      // Exclude changes\n      if (block.excludeAdded) {\n        for (const term of block.excludeAdded) {\n          lines.push(`    + [exclude] ${term}`);\n        }\n      }\n      if (block.excludeRemoved) {\n        for (const term of block.excludeRemoved) {\n          lines.push(`    - [exclude] ${term}`);\n        }\n      }\n    }\n  }\n\n  // Format filter changes\n  const hasFilterChanges =\n    queryDiff.filters.yearFromChanged ||\n    queryDiff.filters.yearToChanged ||\n    queryDiff.filters.languagesAdded.length > 0 ||\n    queryDiff.filters.languagesRemoved.length > 0;\n\n  if (hasFilterChanges) {\n    lines.push('');\n    lines.push('  Filters:');\n\n    if (queryDiff.filters.yearFromChanged) {\n      const oldVal = queryDiff.filters.oldYearFrom ?? '(none)';\n      const newVal = queryDiff.filters.newYearFrom ?? '(none)';\n      lines.push(`    yearFrom: ${oldVal} → ${newVal}`);\n    }\n\n    if (queryDiff.filters.yearToChanged) {\n      const oldVal = queryDiff.filters.oldYearTo ?? '(none)';\n      const newVal = queryDiff.filters.newYearTo ?? 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session1Keys.add(key);\n    }\n  }\n\n  // Build a set of all identifier keys from session2\n  const session2Keys = new Set<string>();\n  for (const article of session2) {\n    for (const key of getArticleKeys(article)) {\n      session2Keys.add(key);\n    }\n  }\n\n  // Classify session1 articles as common or removed\n  const common: Article[] = [];\n  const removed: Article[] = [];\n  for (const article of session1) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as removed\n      removed.push(article);\n      continue;\n    }\n    const isInSession2 = keys.some((key) => session2Keys.has(key));\n    if (isInSession2) {\n      common.push(article);\n    } else {\n      removed.push(article);\n    }\n  }\n\n  // Classify session2 articles as added (those not in session1)\n  const added: Article[] = [];\n  for (const article of session2) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n  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package/dist/cli/commands/fulltext/attach.js

@@ -1,7 +1,7 @@
 import { readFile } from "node:fs/promises";
 import { join } from "node:path";
 import { refExport, refFulltextAttach } from "../../../integration/ref-cli.js";
-import { processFulltextEntries } from "../../../fulltext/attach-shared.js";
+import { processFulltextEntries } from "../../../integration/attach-shared.js";
 async function buildRefLookupFromLibrary(libraryPath, refCliOptions) {
   const lookup = /* @__PURE__ */ new Map();
   try {

package/dist/cli/commands/fulltext/attach.js.map

@@ -1 +1 @@
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package/dist/cli/commands/fulltext/check.d.ts

@@ -1,5 +1,4 @@
-import { DiscoveryConfig } from '../../../fulltext/discovery/index';
-import { OAStatus } from '../../../fulltext/types';
+import { DiscoveryConfig, OAStatus } from '@ncukondo/academic-fulltext';
 export interface FulltextCheckOptions {
     sessionDir: string;
     config: DiscoveryConfig;

package/dist/cli/commands/fulltext/check.d.ts.map

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package/dist/cli/commands/fulltext/check.js

@@ -1,8 +1,10 @@
 import { readFile, access, readdir } from "node:fs/promises";
 import { join } from "node:path";
 import { parse } from "yaml";
-import { discoverOA } from "../../../fulltext/discovery/index.js";
-import { loadMeta, saveMeta } from "../../../fulltext/meta.js";
+import { discoverOA } from "../../../node_modules/@ncukondo/academic-fulltext/dist/discovery/index.js";
+import { loadMeta, saveMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import "node:crypto";
 const DEFAULT_CONCURRENCY = 3;
 async function loadIncludedArticles(sessionDir) {
   const reviewsPath = join(sessionDir, ".internal", "reviews.yaml");

package/dist/cli/commands/fulltext/check.js.map

@@ -1 +1 @@
-{"version":3,"file":"check.js","sources":["../../../../src/cli/commands/fulltext/check.ts"],"sourcesContent":["/**\n * Fulltext check command.\n * Checks OA availability for included articles in a session.\n */\n\nimport { readFile, readdir, access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { discoverOA, type DiscoveryConfig, type DiscoveryArticle } from '../../../fulltext/discovery/index';\nimport { loadMeta, saveMeta } from '../../../fulltext/meta';\nimport type { OAStatus } from '../../../fulltext/types';\nimport type { ReviewFile, ArticleEntry } from '../review/types';\n\n/** Default concurrency for parallel article processing */\nconst DEFAULT_CONCURRENCY = 3;\n\nexport interface FulltextCheckOptions {\n  sessionDir: string;\n  config: DiscoveryConfig;\n  concurrency?: number;\n}\n\nexport interface FulltextCheckArticleResult {\n  doi?: string;\n  pmid?: string;\n  title: string;\n  oaStatus: OAStatus;\n  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let entries: string[];\n  try {\n    const dirEntries = await readdir(fulltextDir);\n    entries = dirEntries.map(String);\n  } catch {\n    return null;\n  }\n\n  for (const entry of entries) {\n    try {\n      const metaPath = join(fulltextDir, entry, 'meta.json');\n      const meta = await loadMeta(metaPath);\n      // Match by DOI or PMID\n      if (article.doi && meta.doi === article.doi) return entry;\n      if (article.pmid && meta.pmid === article.pmid) return entry;\n    } catch {\n      // Skip entries without valid meta.json\n    }\n  }\n  return null;\n}\n\n/**\n * Process a single article: run OA discovery and optionally update meta.json.\n */\nasync function processArticle(\n  article: ArticleEntry,\n  sessionDir: string,\n  config: DiscoveryConfig\n): Promise<FulltextCheckArticleResult> {\n  const discoveryArticle: DiscoveryArticle = {};\n  if (article.doi) discoveryArticle.doi = article.doi;\n  if (article.pmid) discoveryArticle.pmid = article.pmid;\n  if 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articleResult;\n}\n\n/**\n * Run async tasks with a concurrency limit.\n */\nasync function runWithConcurrency<T>(\n  tasks: Array<() => Promise<T>>,\n  concurrency: number\n): Promise<PromiseSettledResult<T>[]> {\n  const results: PromiseSettledResult<T>[] = new Array(tasks.length);\n  let nextIndex = 0;\n\n  async function worker(): Promise<void> {\n    while (nextIndex < tasks.length) {\n      const index = nextIndex++;\n      try {\n        const value = await tasks[index]!();\n        results[index] = { status: 'fulfilled', value };\n      } catch (reason) {\n        results[index] = { status: 'rejected', reason };\n      }\n    }\n  }\n\n  const workers = Array.from({ length: Math.min(concurrency, tasks.length) }, () => worker());\n  await Promise.all(workers);\n  return results;\n}\n\n/**\n * Execute the fulltext check command.\n * Checks OA availability for all included articles in a session,\n * processing articles in parallel with a concurrency limit.\n */\nexport async 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+{"version":3,"file":"check.js","sources":["../../../../src/cli/commands/fulltext/check.ts"],"sourcesContent":["/**\n * Fulltext check command.\n * Checks OA availability for included articles in a session.\n */\n\nimport { readFile, readdir, access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { discoverOA, loadMeta, saveMeta, type DiscoveryConfig, type DiscoveryArticle, type OAStatus } from '@ncukondo/academic-fulltext';\nimport type { ReviewFile, ArticleEntry } from '../review/types';\n\n/** Default concurrency for parallel article processing */\nconst DEFAULT_CONCURRENCY = 3;\n\nexport interface FulltextCheckOptions {\n  sessionDir: string;\n  config: DiscoveryConfig;\n  concurrency?: number;\n}\n\nexport interface FulltextCheckArticleResult {\n  doi?: string;\n  pmid?: string;\n  title: string;\n  oaStatus: OAStatus;\n  locationCount: number;\n}\n\nexport interface FulltextCheckResult {\n  summary: {\n    total: number;\n    open: number;\n    closed: number;\n    unknown: number;\n  };\n  articles: FulltextCheckArticleResult[];\n}\n\n/**\n * Load included articles from reviews.yaml\n */\nasync function loadIncludedArticles(sessionDir: string): Promise<ArticleEntry[]> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(content) as ReviewFile;\n  return reviewFile.articles.filter((a) => a.finalDecision === 'include');\n}\n\n/**\n * Try to find a meta.json matching an article in the fulltext directory.\n * Returns the dirName if found, null otherwise.\n */\nasync function findArticleDir(\n  sessionDir: string,\n  article: ArticleEntry\n): Promise<string | null> {\n  const fulltextDir = join(sessionDir, 'fulltext');\n  try {\n    await access(fulltextDir);\n  } catch {\n    return null;\n  }\n\n  let entries: string[];\n  try {\n    const dirEntries = await readdir(fulltextDir);\n    entries = dirEntries.map(String);\n  } catch {\n    return null;\n  }\n\n  for (const entry of entries) {\n    try {\n      const metaPath = join(fulltextDir, entry, 'meta.json');\n      const meta = await loadMeta(metaPath);\n      // Match by DOI or PMID\n      if (article.doi && meta.doi === article.doi) return entry;\n      if (article.pmid && meta.pmid === article.pmid) return entry;\n    } catch {\n      // Skip entries without valid meta.json\n    }\n  }\n  return null;\n}\n\n/**\n * Process a single article: run OA discovery and optionally update meta.json.\n */\nasync function processArticle(\n  article: ArticleEntry,\n  sessionDir: string,\n  config: DiscoveryConfig\n): Promise<FulltextCheckArticleResult> {\n  const discoveryArticle: DiscoveryArticle = {};\n  if (article.doi) discoveryArticle.doi = article.doi;\n  if (article.pmid) discoveryArticle.pmid = article.pmid;\n  if (article.arxivId) discoveryArticle.arxivId = article.arxivId;\n  const discoveryResult = await discoverOA(discoveryArticle, config);\n\n  const articleResult: FulltextCheckArticleResult = {\n    title: article.title,\n    oaStatus: discoveryResult.oaStatus,\n    locationCount: discoveryResult.locations.length,\n  };\n  if (article.doi) articleResult.doi = article.doi;\n  if (article.pmid) articleResult.pmid = article.pmid;\n\n  // Try to update meta.json if a fulltext directory exists for this article\n  const dirName = await findArticleDir(sessionDir, article);\n  if (dirName) {\n    try {\n      const metaPath = join(sessionDir, 'fulltext', dirName, 'meta.json');\n      const meta = await loadMeta(metaPath);\n      meta.oaStatus = discoveryResult.oaStatus;\n      meta.oaLocations = discoveryResult.locations;\n      meta.checkedAt = new Date().toISOString();\n      await saveMeta(metaPath, meta);\n    } catch {\n      // Meta update is best-effort\n    }\n  }\n\n  return articleResult;\n}\n\n/**\n * Run async tasks with a concurrency limit.\n */\nasync function runWithConcurrency<T>(\n  tasks: Array<() => Promise<T>>,\n  concurrency: number\n): Promise<PromiseSettledResult<T>[]> {\n  const results: PromiseSettledResult<T>[] = new Array(tasks.length);\n  let nextIndex = 0;\n\n  async function worker(): Promise<void> {\n    while (nextIndex < tasks.length) {\n      const index = nextIndex++;\n      try {\n        const value = await tasks[index]!();\n        results[index] = { status: 'fulfilled', value };\n      } catch (reason) {\n        results[index] = { status: 'rejected', reason };\n      }\n    }\n  }\n\n  const workers = Array.from({ length: Math.min(concurrency, tasks.length) }, () => worker());\n  await Promise.all(workers);\n  return results;\n}\n\n/**\n * Execute the fulltext check command.\n * Checks OA availability for all included articles in a session,\n * processing articles in parallel with a concurrency limit.\n */\nexport async function executeFulltextCheck(\n  options: FulltextCheckOptions\n): Promise<FulltextCheckResult> 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package/dist/cli/commands/fulltext/convert.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/fulltext/convert.ts"],"names":[],"mappings":"AAAA;;GAEG;AAMH,MAAM,WAAW,sBAAsB;IACrC,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,GAAG,SAAS,GAAG,QAAQ,CAAC;IAC3C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,oBAAoB,EAAE,CAAC;CAClC;AAwCD,wBAAsB,sBAAsB,CAC1C,OAAO,EAAE,sBAAsB,EAC/B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,oBAAoB,CAAC,CA+D/B"}

package/dist/cli/commands/fulltext/convert.js

@@ -1,7 +1,8 @@
 import { readdir, stat } from "node:fs/promises";
 import { join } from "node:path";
-import { getArticleDir, getMetaPath, getFulltextDir } from "../../../fulltext/paths.js";
-import { convertPmcXmlToMarkdown } from "../../../fulltext/convert/index.js";
+import { getArticleDir, getMetaPath, getFulltextDir } from "../../../node_modules/@ncukondo/academic-fulltext/dist/paths.js";
+import { convertPmcXmlToMarkdown, convertArxivHtmlToMarkdown } from "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/index.js";
+import "node:crypto";
 async function fileExists(path) {
   try {
     await stat(path);
@@ -36,9 +37,12 @@ async function executeFulltextConvert(options, sessionsDir) {
   for (const dirName of articleDirs) {
     const articleDir = getArticleDir(sessionDir, dirName);
     const xmlPath = join(articleDir, "fulltext.xml");
+    const htmlPath = join(articleDir, "fulltext.html");
     const mdPath = join(articleDir, "fulltext.md");
     const metaPath = getMetaPath(sessionDir, dirName);
-    if (!await fileExists(xmlPath)) {
+    const hasXml = await fileExists(xmlPath);
+    const hasHtml = await fileExists(htmlPath);
+    if (!hasXml && !hasHtml) {
       continue;
     }
     if (await fileExists(mdPath)) {
@@ -47,11 +51,7 @@ async function executeFulltextConvert(options, sessionsDir) {
       continue;
     }
     const metaPathExists = await fileExists(metaPath);
-    const result = await convertPmcXmlToMarkdown(
-      xmlPath,
-      mdPath,
-      metaPathExists ? metaPath : void 0
-    );
+    const result = hasXml ? await convertPmcXmlToMarkdown(xmlPath, mdPath, metaPathExists ? metaPath : void 0) : await convertArxivHtmlToMarkdown(htmlPath, mdPath, metaPathExists ? metaPath : void 0);
     if (result.success) {
       converted++;
       articles.push({

package/dist/cli/commands/fulltext/convert.js.map

@@ -1 +1 @@
-{"version":3,"file":"convert.js","sources":["../../../../src/cli/commands/fulltext/convert.ts"],"sourcesContent":["/**\n * Fulltext convert command - converts PMC XML to Markdown.\n */\n\nimport { readdir, stat } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { getFulltextDir, getArticleDir, getMetaPath } from '../../../fulltext/paths.js';\nimport { convertPmcXmlToMarkdown } from '../../../fulltext/convert/index.js';\n\nexport interface FulltextConvertOptions {\n  sessionId: string;\n  article?: string;\n}\n\nexport interface ConvertArticleResult {\n  dirName: string;\n  title: string;\n  status: 'converted' | 'skipped' | 'failed';\n  error?: string;\n}\n\nexport interface ConvertCommandResult {\n  success: boolean;\n  converted: number;\n  skipped: number;\n  failed: number;\n  articles: ConvertArticleResult[];\n}\n\nasync function fileExists(path: string): Promise<boolean> {\n  try {\n    await stat(path);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Get list of article directory names to process.\n */\nasync function getArticleDirs(\n  sessionDir: string,\n  articleFilter?: string,\n): Promise<string[]> {\n  const fulltextDir = getFulltextDir(sessionDir);\n\n  if (articleFilter) {\n    // Filter to specific article\n    const articlePath = getArticleDir(sessionDir, articleFilter);\n    if (await fileExists(articlePath)) {\n      return [articleFilter];\n    }\n    return [];\n  }\n\n  // List all directories in fulltext/\n  try {\n    const entries = await readdir(fulltextDir, { withFileTypes: true });\n    return entries\n      .filter((e) => e.isDirectory())\n      .map((e) => e.name);\n  } catch {\n    return [];\n  }\n}\n\nexport async function executeFulltextConvert(\n  options: FulltextConvertOptions,\n  sessionsDir: string,\n): Promise<ConvertCommandResult> {\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const articleDirs = await getArticleDirs(sessionDir, options.article);\n\n  const articles: ConvertArticleResult[] = [];\n  let converted = 0;\n  let skipped = 0;\n  let failed = 0;\n\n  for (const dirName of articleDirs) {\n    const articleDir = getArticleDir(sessionDir, dirName);\n    const xmlPath = join(articleDir, 'fulltext.xml');\n    const mdPath = join(articleDir, 'fulltext.md');\n    const metaPath = getMetaPath(sessionDir, dirName);\n\n    // Check if XML exists\n    if (!(await fileExists(xmlPath))) {\n      continue; // No XML to convert, skip silently\n    }\n\n    // Check if already converted\n    if (await fileExists(mdPath)) {\n      skipped++;\n      articles.push({ dirName, title: dirName, status: 'skipped' });\n      continue;\n    }\n\n    // Convert\n    const metaPathExists = await fileExists(metaPath);\n    const result = await convertPmcXmlToMarkdown(\n      xmlPath,\n      mdPath,\n      metaPathExists ? metaPath : undefined,\n    );\n\n    if (result.success) {\n      converted++;\n      articles.push({\n        dirName,\n        title: result.title ?? dirName,\n        status: 'converted',\n      });\n    } else {\n      failed++;\n      const articleResult: ConvertArticleResult = {\n        dirName,\n        title: dirName,\n        status: 'failed',\n      };\n      if (result.error) articleResult.error = result.error;\n      articles.push(articleResult);\n    }\n  }\n\n  return {\n    success: failed === 0,\n    converted,\n    skipped,\n    failed,\n    articles,\n  };\n}\n"],"names":[],"mappings":";;;;AA6BA,eAAe,WAAW,MAAgC;AACxD,MAAI;AACF,UAAM,KAAK,IAAI;AACf,WAAO;AAAA,EACT,QAAQ;AACN,WAAO;AAAA,EACT;AACF;AAKA,eAAe,eACb,YACA,eACmB;AACnB,QAAM,cAAc,eAAe,UAAU;AAE7C,MAAI,eAAe;AAEjB,UAAM,cAAc,cAAc,YAAY,aAAa;AAC3D,QAAI,MAAM,WAAW,WAAW,GAAG;AACjC,aAAO,CAAC,aAAa;AAAA,IACvB;AACA,WAAO,CAAA;AAAA,EACT;AAGA,MAAI;AACF,UAAM,UAAU,MAAM,QAAQ,aAAa,EAAE,eAAe,MAAM;AAClE,WAAO,QACJ,OAAO,CAAC,MAAM,EAAE,aAAa,EAC7B,IAAI,CAAC,MAAM,EAAE,IAAI;AAAA,EACtB,QAAQ;AACN,WAAO,CAAA;AAAA,EACT;AACF;AAEA,eAAsB,uBACpB,SACA,aAC+B;AAC/B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AACtD,QAAM,cAAc,MAAM,eAAe,YAAY,QAAQ,OAAO;AAEpE,QAAM,WAAmC,CAAA;AACzC,MAAI,YAAY;AAChB,MAAI,UAAU;AACd,MAAI,SAAS;AAEb,aAAW,WAAW,aAAa;AACjC,UAAM,aAAa,cAAc,YAAY,OAAO;AACpD,UAAM,UAAU,KAAK,YAAY,cAAc;AAC/C,UAAM,SAAS,KAAK,YAAY,aAAa;AAC7C,UAAM,WAAW,YAAY,YAAY,OAAO;AAGhD,QAAI,CAAE,MAAM,WAAW,OAAO,GAAI;AAChC;AAAA,IACF;AAGA,QAAI,MAAM,WAAW,MAAM,GAAG;AAC5B;AACA,eAAS,KAAK,EAAE,SAAS,OAAO,SAAS,QAAQ,WAAW;AAC5D;AAAA,IACF;AAGA,UAAM,iBAAiB,MAAM,WAAW,QAAQ;AAChD,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,MACA;AAAA,MACA,iBAAiB,WAAW;AAAA,IAAA;AAG9B,QAAI,OAAO,SAAS;AAClB;AACA,eAAS,KAAK;AAAA,QACZ;AAAA,QACA,OAAO,OAAO,SAAS;AAAA,QACvB,QAAQ;AAAA,MAAA,CACT;AAAA,IACH,OAAO;AACL;AACA,YAAM,gBAAsC;AAAA,QAC1C;AAAA,QACA,OAAO;AAAA,QACP,QAAQ;AAAA,MAAA;AAEV,UAAI,OAAO,MAAO,eAAc,QAAQ,OAAO;AAC/C,eAAS,KAAK,aAAa;AAAA,IAC7B;AAAA,EACF;AAEA,SAAO;AAAA,IACL,SAAS,WAAW;AAAA,IACpB;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EAAA;AAEJ;"}
+{"version":3,"file":"convert.js","sources":["../../../../src/cli/commands/fulltext/convert.ts"],"sourcesContent":["/**\n * Fulltext convert command - converts PMC XML to Markdown.\n */\n\nimport { readdir, stat } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { getFulltextDir, getArticleDir, getMetaPath, convertPmcXmlToMarkdown, convertArxivHtmlToMarkdown } from '@ncukondo/academic-fulltext';\n\nexport interface FulltextConvertOptions {\n  sessionId: string;\n  article?: string;\n}\n\nexport interface ConvertArticleResult {\n  dirName: string;\n  title: string;\n  status: 'converted' | 'skipped' | 'failed';\n  error?: string;\n}\n\nexport interface ConvertCommandResult {\n  success: boolean;\n  converted: number;\n  skipped: number;\n  failed: number;\n  articles: ConvertArticleResult[];\n}\n\nasync function fileExists(path: string): Promise<boolean> {\n  try {\n    await stat(path);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Get list of article directory names to process.\n */\nasync function getArticleDirs(\n  sessionDir: string,\n  articleFilter?: string,\n): Promise<string[]> {\n  const fulltextDir = getFulltextDir(sessionDir);\n\n  if (articleFilter) {\n    // Filter to specific article\n    const articlePath = getArticleDir(sessionDir, articleFilter);\n    if (await fileExists(articlePath)) {\n      return [articleFilter];\n    }\n    return [];\n  }\n\n  // List all directories in fulltext/\n  try {\n    const entries = await readdir(fulltextDir, { withFileTypes: true });\n    return entries\n      .filter((e) => e.isDirectory())\n      .map((e) => e.name);\n  } catch {\n    return [];\n  }\n}\n\nexport async function executeFulltextConvert(\n  options: FulltextConvertOptions,\n  sessionsDir: string,\n): Promise<ConvertCommandResult> {\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const articleDirs = await getArticleDirs(sessionDir, options.article);\n\n  const articles: ConvertArticleResult[] = [];\n  let converted = 0;\n  let skipped = 0;\n  let failed = 0;\n\n  for (const dirName of articleDirs) {\n    const articleDir = getArticleDir(sessionDir, dirName);\n    const xmlPath = join(articleDir, 'fulltext.xml');\n    const htmlPath = join(articleDir, 'fulltext.html');\n    const mdPath = join(articleDir, 'fulltext.md');\n    const metaPath = getMetaPath(sessionDir, dirName);\n\n    const hasXml = await fileExists(xmlPath);\n    const hasHtml = await fileExists(htmlPath);\n\n    // No convertible source found\n    if (!hasXml && !hasHtml) {\n      continue;\n    }\n\n    // Check if already converted\n    if (await fileExists(mdPath)) {\n      skipped++;\n      articles.push({ dirName, title: dirName, status: 'skipped' });\n      continue;\n    }\n\n    // Convert: prefer PMC XML, fall back to arXiv HTML\n    const metaPathExists = await fileExists(metaPath);\n    const result = hasXml\n      ? await convertPmcXmlToMarkdown(xmlPath, mdPath, metaPathExists ? metaPath : undefined)\n      : await convertArxivHtmlToMarkdown(htmlPath, mdPath, metaPathExists ? metaPath : undefined);\n\n    if (result.success) {\n      converted++;\n      articles.push({\n        dirName,\n        title: result.title ?? dirName,\n        status: 'converted',\n      });\n    } else {\n      failed++;\n      const articleResult: ConvertArticleResult = {\n        dirName,\n        title: dirName,\n        status: 'failed',\n      };\n      if (result.error) articleResult.error = result.error;\n      articles.push(articleResult);\n    }\n  }\n\n  return {\n    success: failed === 0,\n    converted,\n    skipped,\n    failed,\n    articles,\n  };\n}\n"],"names":[],"mappings":";;;;;AA4BA,eAAe,WAAW,MAAgC;AACxD,MAAI;AACF,UAAM,KAAK,IAAI;AACf,WAAO;AAAA,EACT,QAAQ;AACN,WAAO;AAAA,EACT;AACF;AAKA,eAAe,eACb,YACA,eACmB;AACnB,QAAM,cAAc,eAAe,UAAU;AAE7C,MAAI,eAAe;AAEjB,UAAM,cAAc,cAAc,YAAY,aAAa;AAC3D,QAAI,MAAM,WAAW,WAAW,GAAG;AACjC,aAAO,CAAC,aAAa;AAAA,IACvB;AACA,WAAO,CAAA;AAAA,EACT;AAGA,MAAI;AACF,UAAM,UAAU,MAAM,QAAQ,aAAa,EAAE,eAAe,MAAM;AAClE,WAAO,QACJ,OAAO,CAAC,MAAM,EAAE,aAAa,EAC7B,IAAI,CAAC,MAAM,EAAE,IAAI;AAAA,EACtB,QAAQ;AACN,WAAO,CAAA;AAAA,EACT;AACF;AAEA,eAAsB,uBACpB,SACA,aAC+B;AAC/B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AACtD,QAAM,cAAc,MAAM,eAAe,YAAY,QAAQ,OAAO;AAEpE,QAAM,WAAmC,CAAA;AACzC,MAAI,YAAY;AAChB,MAAI,UAAU;AACd,MAAI,SAAS;AAEb,aAAW,WAAW,aAAa;AACjC,UAAM,aAAa,cAAc,YAAY,OAAO;AACpD,UAAM,UAAU,KAAK,YAAY,cAAc;AAC/C,UAAM,WAAW,KAAK,YAAY,eAAe;AACjD,UAAM,SAAS,KAAK,YAAY,aAAa;AAC7C,UAAM,WAAW,YAAY,YAAY,OAAO;AAEhD,UAAM,SAAS,MAAM,WAAW,OAAO;AACvC,UAAM,UAAU,MAAM,WAAW,QAAQ;AAGzC,QAAI,CAAC,UAAU,CAAC,SAAS;AACvB;AAAA,IACF;AAGA,QAAI,MAAM,WAAW,MAAM,GAAG;AAC5B;AACA,eAAS,KAAK,EAAE,SAAS,OAAO,SAAS,QAAQ,WAAW;AAC5D;AAAA,IACF;AAGA,UAAM,iBAAiB,MAAM,WAAW,QAAQ;AAChD,UAAM,SAAS,SACX,MAAM,wBAAwB,SAAS,QAAQ,iBAAiB,WAAW,MAAS,IACpF,MAAM,2BAA2B,UAAU,QAAQ,iBAAiB,WAAW,MAAS;AAE5F,QAAI,OAAO,SAAS;AAClB;AACA,eAAS,KAAK;AAAA,QACZ;AAAA,QACA,OAAO,OAAO,SAAS;AAAA,QACvB,QAAQ;AAAA,MAAA,CACT;AAAA,IACH,OAAO;AACL;AACA,YAAM,gBAAsC;AAAA,QAC1C;AAAA,QACA,OAAO;AAAA,QACP,QAAQ;AAAA,MAAA;AAEV,UAAI,OAAO,MAAO,eAAc,QAAQ,OAAO;AAC/C,eAAS,KAAK,aAAa;AAAA,IAC7B;AAAA,EACF;AAEA,SAAO;AAAA,IACL,SAAS,WAAW;AAAA,IACpB;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EAAA;AAEJ;"}

package/dist/cli/commands/fulltext/fetch.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/fulltext/fetch.js

@@ -1,8 +1,10 @@
 import { join } from "node:path";
 import { readFile, writeFile } from "node:fs/promises";
 import { parse, stringify } from "yaml";
-import { loadMeta } from "../../../fulltext/meta.js";
-import { fetchAllFulltexts } from "../../../fulltext/download/orchestrator.js";
+import { fetchAllFulltexts } from "../../../node_modules/@ncukondo/academic-fulltext/dist/download/orchestrator.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import { loadMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import "node:crypto";
 import { executeFulltextConvert } from "./convert.js";
 async function executeFulltextFetch(options) {
   const { sessionId, sessionsDir, source, dryRun, concurrency = 3, retryDelay = 1e3 } = options;
@@ -42,7 +44,8 @@ async function executeFulltextFetch(options) {
     toFetch.push({
       dirName,
       oaLocations: locations,
-      ...meta.pmcid ? { pmcid: meta.pmcid } : {}
+      ...meta.pmcid ? { pmcid: meta.pmcid } : {},
+      ...meta.arxivId ? { arxivId: meta.arxivId } : {}
     });
   }
   if (dryRun) {
@@ -65,10 +68,10 @@ async function executeFulltextFetch(options) {
   const results = await fetchAllFulltexts(toFetch, sessionDir, fetchOpts);
   const convertMarkdown = options.convertMarkdown !== false;
   if (convertMarkdown) {
-    const xmlArticles = results.filter(
-      (r) => r.status === "downloaded" && r.filesDownloaded?.includes("fulltext.xml")
+    const convertibleArticles = results.filter(
+      (r) => r.status === "downloaded" && (r.filesDownloaded?.includes("fulltext.xml") || r.filesDownloaded?.includes("fulltext.html"))
     );
-    for (const article of xmlArticles) {
+    for (const article of convertibleArticles) {
       await executeFulltextConvert({ sessionId, article: article.dirName }, sessionsDir);
     }
   }
@@ -111,6 +114,7 @@ async function updateReviews(sessionDir, results) {
           article.fulltext.hasFiles = {
             pdf: article.fulltext.hasFiles.pdf || result.filesDownloaded.includes("fulltext.pdf"),
             xml: article.fulltext.hasFiles.xml || result.filesDownloaded.includes("fulltext.xml"),
+            html: article.fulltext.hasFiles.html || result.filesDownloaded.includes("fulltext.html"),
             markdown: article.fulltext.hasFiles.markdown || result.filesDownloaded.includes("fulltext.md")
           };
           changed = true;

package/dist/cli/commands/fulltext/fetch.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetch.js","sources":["../../../../src/cli/commands/fulltext/fetch.ts"],"sourcesContent":["/**\n * Fulltext fetch command - downloads OA fulltexts for session articles.\n */\n\nimport { join } from 'node:path';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { ReviewFile } from '../review/types.js';\nimport { loadMeta, fetchAllFulltexts, type FulltextMeta, type FetchArticle } from '@ncukondo/academic-fulltext';\nimport { executeFulltextConvert } from './convert.js';\nexport interface FulltextFetchOptions {\n  sessionId: string;\n  sessionsDir: string;\n  source?: string[];\n  convertMarkdown?: boolean;\n  dryRun?: boolean;\n  concurrency?: number;\n  retryDelay?: number;\n}\n\nexport interface FulltextFetchArticle {\n  dirName: string;\n  title: string;\n  oaStatus: string;\n  locationCount: number;\n}\n\nexport interface FulltextFetchResult {\n  summary: {\n    total: number;\n    downloaded: number;\n    failed: number;\n    skipped: number;\n  };\n  articles: FulltextFetchArticle[];\n  dryRun?: boolean;\n}\n\n/**\n * Execute the fulltext fetch command.\n * Loads articles from reviews.yaml, checks OA status via meta.json,\n * and downloads PDFs/XMLs from OA sources.\n */\nexport async function executeFulltextFetch(\n  options: FulltextFetchOptions,\n): Promise<FulltextFetchResult> {\n  const { sessionId, sessionsDir, source, dryRun, concurrency = 3, retryDelay = 1000 } = options;\n  const sessionDir = join(sessionsDir, sessionId);\n\n  // Load reviews.yaml to find articles with fulltext dirs\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const reviewContent = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(reviewContent) as ReviewFile;\n\n  const includedArticles = reviewFile.articles.filter(\n    (a) => a.finalDecision === 'include' && a.fulltext?.dirName,\n  );\n\n  // Load meta.json for each article to check OA status\n  const toFetch: FetchArticle[] = [];\n  const allArticles: FulltextFetchArticle[] = [];\n  let skippedCount = 0;\n\n  const fulltextDir = join(sessionDir, 'fulltext');\n  for (const article of includedArticles) {\n    const dirName = article.fulltext?.dirName;\n    if (!dirName) continue;\n\n    let meta: FulltextMeta;\n    try {\n      const metaPath = join(fulltextDir, dirName, 'meta.json');\n      meta = await loadMeta(metaPath);\n    } catch {\n      skippedCount++;\n      continue;\n    }\n\n    const locations = meta.oaLocations ?? 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package/dist/cli/commands/fulltext/index.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/fulltext/index.js

@@ -168,6 +168,8 @@ Fulltext ${prefix.toLowerCase()}:`);
         config: {
           unpaywallEmail: config.fulltext?.sources?.unpaywall_email ?? "",
           coreApiKey: config.fulltext?.sources?.core_api_key ?? "",
+          ncbiEmail: config.fulltext?.sources?.ncbi_email ?? "",
+          ncbiTool: config.fulltext?.sources?.ncbi_tool ?? "search-hub",
           preferSources: config.fulltext?.sources?.prefer_sources ?? ["pmc", "arxiv", "unpaywall", "core"]
         }
       });

package/dist/cli/commands/fulltext/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../../../../src/cli/commands/fulltext/index.ts"],"sourcesContent":["/**\n * Fulltext command group registration.\n */\n\nimport type { Command } from 'commander';\nimport { executeFulltextInit } from './init.js';\nimport { executeFulltextSync } from './sync.js';\nimport { executeFulltextConvert } from './convert.js';\nimport { executeFulltextCheck } from './check.js';\nimport { executeFulltextFetch } from './fetch.js';\nimport { executeFulltextAttach } from './attach.js';\nimport { executeFulltextStatus, type FulltextStatusResult } from './status.js';\nimport { executeFulltextPending, type PendingArticle } from './pending.js';\nimport { formatInitOutput, formatSyncOutput } from './format.js';\nimport type { GlobalOptions } from '../../index.js';\nimport { EXIT_CODES } from '../../exit-codes.js';\nimport { sessionExists } from '../../../session/manager.js';\nimport { loadConfig } from '../../../config/index.js';\nimport { join } from 'node:path';\n\nexport function registerFulltextCommands(\n  program: Command,\n  getSessionsDir: (opts: GlobalOptions) => Promise<string>,\n): void {\n  const fulltextCommand = program\n    .command('fulltext')\n    .description('Fulltext management: retrieval, conversion, attachment')\n    .addHelpText('after', `\nExamples:\n  $ search-hub fulltext init SESSION_ID               # Create directories for included articles\n  $ search-hub fulltext init SESSION_ID --dry-run     # Preview what would be created\n  $ search-hub fulltext sync SESSION_ID               # Detect and register added files\n  $ search-hub fulltext sync SESSION_ID --dry-run     # Preview what would be synced\n  $ search-hub fulltext convert SESSION_ID            # Convert PMC XML to Markdown\n  $ search-hub fulltext check --session SESSION_ID   # Check OA availability\n  $ search-hub fulltext fetch SESSION_ID              # Download available OA articles\n  $ search-hub fulltext fetch SESSION_ID --dry-run    # Preview what would be downloaded\n  $ search-hub fulltext fetch SESSION_ID --source pmc # Download from specific sources\n  $ search-hub fulltext attach SESSION_ID             # Attach fulltexts to ref entries\n  $ search-hub fulltext attach SESSION_ID --dry-run   # Preview what would be attached\n  $ search-hub fulltext status SESSION_ID            # Show fulltext retrieval status\n  $ search-hub fulltext pending SESSION_ID           # List articles needing download`);\n\n  fulltextCommand\n    .command('init')\n    .description('Create directories for included articles with meta.json and README')\n    .argument('<session-id>', 'session ID')\n    .option('--dry-run', 'show what would be created without creating', false)\n    .action(async (sessionId: string, options: { dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n\n        const result = await executeFulltextInit({\n          sessionId,\n          sessionsDir,\n          dryRun: options.dryRun,\n        });\n\n        if (!globalOpts.quiet) {\n          console.log(formatInitOutput(result));\n        }\n\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error,\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('sync')\n    .description('Detect and register manually added fulltext files')\n    .argument('<session-id>', 'session ID')\n    .option('--dry-run', 'show what would be synced without modifying', false)\n    .action(async (sessionId: string, options: { dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n\n        const result = await executeFulltextSync({\n          sessionId,\n          sessionsDir,\n          dryRun: options.dryRun,\n        });\n\n        if (!globalOpts.quiet) {\n          console.log(formatSyncOutput(result));\n        }\n\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error,\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('convert')\n    .description('Convert PMC XML files to Markdown')\n    .argument('<session-id>', 'session ID')\n    .option('--article <dir>', 'convert specific article directory')\n    .action(async (sessionId: string, options?: { article?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        const convertOpts: Parameters<typeof executeFulltextConvert>[0] = { sessionId };\n        if (options?.article) convertOpts.article = options.article;\n        const result = await executeFulltextConvert(convertOpts, sessionsDir);\n\n        if (!globalOpts.quiet) {\n          console.log(`Converted: ${result.converted}  Skipped: ${result.skipped}  Failed: ${result.failed}`);\n          for (const article of result.articles) {\n            const icon = article.status === 'converted' ? '+' : article.status === 'skipped' ? '-' : '!';\n            console.log(`  [${icon}] ${article.dirName}: ${article.title}`);\n          }\n        }\n\n        process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.SESSION_ERROR;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('attach')\n    .description('Attach fulltext files to reference-manager entries')\n    .argument('<session-id>', 'session ID')\n    .option('--dry-run', 'show what would be attached without attaching', false)\n    .action(async (sessionId: string, options: { dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n\n        if (!(await sessionExists(sessionId, sessionsDir))) {\n          if (!globalOpts.quiet) {\n            console.error(`Error: session '${sessionId}' not found`);\n          }\n          process.exitCode = EXIT_CODES.SESSION_ERROR;\n          return;\n        }\n\n        const sessionDir = join(sessionsDir, sessionId);\n\n        const result = await executeFulltextAttach({\n          sessionDir,\n          dryRun: options.dryRun,\n        });\n\n        if (!globalOpts.quiet) {\n          const prefix = options.dryRun ? 'Would attach' : 'Attached';\n          console.log(`\\nFulltext ${prefix.toLowerCase()}:`);\n          if (result.summary.attached > 0) {\n            const totalFiles = result.attached.reduce((sum, a) => sum + a.files.length, 0);\n            console.log(`  ✓ ${result.summary.attached} articles (${totalFiles} files)`);\n            for (const item of result.attached) {\n              console.log(`    ${item.refId}: ${item.files.join(', ')}`);\n            }\n          }\n          if (result.summary.skipped > 0) {\n            console.log(`  ⚠ ${result.summary.skipped} skipped`);\n          }\n          if (result.summary.failed > 0) {\n            console.log(`  ✗ ${result.summary.failed} failed`);\n            for (const item of result.failed) {\n              console.log(`    ${item.dirName}: ${item.reason}`);\n            }\n          }\n          if (result.summary.total === 0) {\n            console.log('  No fulltext directories found.');\n          }\n        }\n\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error(\n            'Error:',\n            error instanceof Error ? error.message : error,\n          );\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('check')\n    .description('Check Open Access availability for included articles')\n    .requiredOption('--session <id>', 'session ID')\n    .option('--format <format>', 'output format (table or json)', 'table')\n    .action(async (options: { session: string; format: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, options.session);\n        const config = await loadConfig(\n          globalOpts.config ? { globalConfigPath: globalOpts.config } : {}\n        );\n        const result = await executeFulltextCheck({\n          sessionDir,\n          config: {\n            unpaywallEmail: config.fulltext?.sources?.unpaywall_email ?? '',\n            coreApiKey: config.fulltext?.sources?.core_api_key ?? '',\n            preferSources: config.fulltext?.sources?.prefer_sources ?? ['pmc', 'arxiv', 'unpaywall', 'core'],\n          },\n        });\n\n        if (options.format === 'json') {\n          console.log(JSON.stringify(result, null, 2));\n        } else if (!globalOpts.quiet) {\n          console.log(`\\nOA Status Summary:`);\n          console.log(`  Open Access:    ${result.summary.open}`);\n          console.log(`  Closed Access:  ${result.summary.closed}`);\n          console.log(`  Unknown:        ${result.summary.unknown}`);\n          console.log(`  Total:          ${result.summary.total}`);\n          if (result.summary.open > 0) {\n            console.log(`\\nRun \\`fulltext fetch\\` to download available OA articles.`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('fetch')\n    .description('Download available OA fulltexts')\n    .argument('<session-id>', 'session ID')\n    .option('--source <sources>', 'filter by source (comma-separated: pmc,arxiv,unpaywall,core)')\n    .option('--no-convert-markdown', 'skip auto-conversion of PMC XML to Markdown')\n    .option('--dry-run', 'show what would be downloaded without downloading', false)\n    .action(async (sessionId: string, options: { source?: string; convertMarkdown: boolean; dryRun: boolean }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n\n        const fetchOpts: Parameters<typeof executeFulltextFetch>[0] = {\n          sessionId,\n          sessionsDir,\n          convertMarkdown: options.convertMarkdown,\n          dryRun: options.dryRun,\n        };\n        if (options.source) fetchOpts.source = options.source.split(',');\n        const result = await executeFulltextFetch(fetchOpts);\n\n        if (!globalOpts.quiet) {\n          if (result.dryRun) {\n            console.log(`\\nDry run: would fetch ${result.articles.length} articles`);\n            for (const article of result.articles) {\n              console.log(`  ${article.dirName}: ${article.title} (${article.locationCount} sources)`);\n            }\n          } else {\n            console.log(`\\nFulltext Fetch Summary:`);\n            console.log(`  Downloaded: ${result.summary.downloaded}`);\n            console.log(`  Failed:     ${result.summary.failed}`);\n            console.log(`  Skipped:    ${result.summary.skipped}`);\n            console.log(`  Total:      ${result.summary.total}`);\n          }\n        }\n\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('status')\n    .description('Show overall fulltext retrieval status')\n    .argument('<session-id>', 'session ID')\n    .option('--format <format>', 'output format (table or json)', 'table')\n    .action(async (sessionId: string, options: { format: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n        const result = await executeFulltextStatus({\n          sessionDir,\n          format: options.format as 'table' | 'json',\n        });\n\n        if (options.format === 'json') {\n          console.log(JSON.stringify(result, null, 2));\n        } else if (!globalOpts.quiet) {\n          console.log(formatStatusOutput(result, sessionId));\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n\n  fulltextCommand\n    .command('pending')\n    .description('List articles needing manual fulltext download')\n    .argument('<session-id>', 'session ID')\n    .option('--format <format>', 'output format (table or json)', 'table')\n    .option('--export <file>', 'export URLs to file for batch download')\n    .action(async (sessionId: string, options: { format: string; export?: string }) => {\n      const globalOpts = program.opts() as GlobalOptions;\n      try {\n        const sessionsDir = await getSessionsDir(globalOpts);\n        const sessionDir = join(sessionsDir, sessionId);\n        const result = await executeFulltextPending({\n          sessionDir,\n          format: options.format as 'table' | 'json',\n          exportPath: options.export,\n        });\n\n        if (options.format === 'json') {\n          console.log(JSON.stringify(result, null, 2));\n        } else if (!globalOpts.quiet) {\n          console.log(formatPendingOutput(result.articles, result.totalPending));\n          if (options.export) {\n            console.log(`\\nExported URLs to ${options.export}`);\n          } else if (result.totalPending > 0) {\n            console.log(`\\nExport URLs: fulltext pending ${sessionId} --export urls.txt`);\n          }\n        }\n        process.exitCode = EXIT_CODES.SUCCESS;\n      } catch (error) {\n        if (!globalOpts.quiet) {\n          console.error('Error:', error instanceof Error ? error.message : error);\n        }\n        process.exitCode = EXIT_CODES.SESSION_ERROR;\n      }\n    });\n}\n\nfunction formatStatusOutput(result: FulltextStatusResult, sessionId: string): string {\n  const lines = [\n    `Fulltext Status: ${sessionId}`,\n    '',\n    `  Included articles: ${result.totalIncluded}`,\n    `  With fulltext:     ${result.withFulltext}`,\n    `    - PDF only:      ${result.pdfOnly}`,\n    `    - Markdown only: ${result.markdownOnly}`,\n    `    - Both:          ${result.both}`,\n    `  Pending:           ${result.pending}  (directories created, no files)`,\n    `  Not initialized:   ${result.notInitialized}  (no directory)`,\n  ];\n  return lines.join('\\n');\n}\n\nfunction formatPendingOutput(articles: PendingArticle[], total: number): string {\n  if (total === 0) {\n    return 'All included articles have fulltext.';\n  }\n\n  const lines: string[] = [`${total} articles need fulltext:`, ''];\n\n  for (const [i, article] of articles.entries()) {\n    const num = i + 1;\n    const identifier = article.dirName ?? '(not initialized)';\n    lines.push(`${num}. ${identifier} - \"${article.title}\"`);\n    if (article.doi) {\n      lines.push(`   DOI: ${article.doi}`);\n    }\n    if (article.publisherUrl) {\n      lines.push(`   Publisher: ${article.publisherUrl}`);\n    }\n    if (article.oaLocations) {\n      for (const loc of article.oaLocations) {\n        lines.push(`   ${loc.source}: ${loc.url}`);\n      }\n    }\n    lines.push('');\n  }\n\n  return 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package/dist/cli/commands/fulltext/init.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/fulltext/init.ts"],"names":[],"mappings":"AAAA;;GAEG;AASH,MAAM,WAAW,mBAAmB;IAClC,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,iBAAiB;IAChC,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,kBAAkB;IACjC,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,mBAAmB,GAC3B,OAAO,CAAC,kBAAkB,CAAC,CA8G7B"}

package/dist/cli/commands/fulltext/init.js

@@ -2,10 +2,11 @@ import { join } from "node:path";
 import { readFile, mkdir, writeFile } from "node:fs/promises";
 import { randomUUID } from "node:crypto";
 import { parse, stringify } from "yaml";
-import { generateCitationKey, generateDirName } from "../../../fulltext/citation-key.js";
-import { createMeta, saveMeta } from "../../../fulltext/meta.js";
-import { generateReadme } from "../../../fulltext/readme.js";
-import { getArticleDir, getMetaPath, getReadmePath, getFulltextDir } from "../../../fulltext/paths.js";
+import { createMeta, saveMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import { getArticleDir, getMetaPath, getReadmePath, getFulltextDir } from "../../../node_modules/@ncukondo/academic-fulltext/dist/paths.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import { generateCitationKey, generateDirName } from "../../../node_modules/@ncukondo/academic-fulltext/dist/citation-key.js";
+import { generateReadme } from "../../../node_modules/@ncukondo/academic-fulltext/dist/readme.js";
 async function executeFulltextInit(options) {
   const { sessionId, sessionsDir, dryRun } = options;
   const sessionDir = join(sessionsDir, sessionId);
@@ -50,7 +51,7 @@ async function executeFulltextInit(options) {
     const meta = createMeta(metaOpts);
     const fulltextRef = {
       dirName,
-      hasFiles: { pdf: false, xml: false, markdown: false }
+      hasFiles: { pdf: false, xml: false, html: false, markdown: false }
     };
     if (!dryRun) {
       const articleDir = getArticleDir(sessionDir, dirName);