@ncukondo/search-hub 0.12.1 → 0.12.2

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  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 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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: 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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 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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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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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+{"version":3,"file":"fetch.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/fulltext/fetch.ts"],"names":[],"mappings":"AAAA;;GAEG;AAQH,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE;QACP,KAAK,EAAE,MAAM,CAAC;QACd,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;QACf,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;IACF,QAAQ,EAAE,oBAAoB,EAAE,CAAC;IACjC,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED;;;;GAIG;AACH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,mBAAmB,CAAC,CAkH9B"}

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 @@
-{"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 type { FulltextMeta } from '../../../fulltext/types.js';\nimport { loadMeta } from '../../../fulltext/meta.js';\nimport { fetchAllFulltexts, type FetchArticle } from '../../../fulltext/download/orchestrator.js';\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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+{"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);

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

@@ -1 +1 @@
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[]).filter(\n    (a) => a.finalDecision === 'include',\n  );\n\n  // Collect existing dirNames from reviews for skip detection\n  const existingDirNames = new Set<string>();\n  for (const article of reviewFile.articles ?? []) {\n    if (article.fulltext?.dirName) {\n      existingDirNames.add(article.fulltext.dirName);\n    }\n  }\n\n  const entries: FulltextInitEntry[] = [];\n  const existingKeys: string[] = [];\n  let created = 0;\n  let skipped = 0;\n\n  // Track which articles in reviewFile to update with fulltext refs\n  const fulltextUpdates = new Map<number, ArticleFulltextRef>();\n\n  for (let i = 0; i < includedArticles.length; i++) {\n    const article = includedArticles[i]!;\n\n    // Find the article's index in the full review file (including non-included)\n    const reviewIndex = reviewFile.articles.indexOf(article);\n\n    // Skip if already has a fulltext directory\n    if (article.fulltext?.dirName && existingDirNames.has(article.fulltext.dirName)) {\n      skipped++;\n      continue;\n    }\n\n    // Generate citation key and directory name\n    const citationKey = generateCitationKey(article.authors, article.year, existingKeys);\n    existingKeys.push(citationKey);\n\n    const uuid = randomUUID();\n    const dirName = generateDirName(citationKey, uuid);\n\n    // Create meta\n    const metaOpts: Parameters<typeof createMeta>[0] = {\n      citationKey,\n      uuid,\n      title: article.title,\n    };\n    if (article.doi) metaOpts.doi = article.doi;\n    if (article.pmid) metaOpts.pmid = article.pmid;\n    if (article.arxivId) metaOpts.arxivId = article.arxivId;\n    if (article.authors) metaOpts.authors = article.authors;\n    if (article.year) metaOpts.year = article.year;\n    const meta = createMeta(metaOpts);\n\n    // Build fulltext ref for reviews.yaml\n    const fulltextRef: ArticleFulltextRef = {\n      dirName,\n      hasFiles: { pdf: false, xml: false, markdown: false },\n    };\n\n    if (!dryRun) {\n      // Create directory\n      const articleDir = getArticleDir(sessionDir, dirName);\n      await mkdir(articleDir, { recursive: true });\n\n      // Write meta.json\n      await saveMeta(getMetaPath(sessionDir, dirName), meta);\n\n      // Write README.md\n      const readme = generateReadme(meta);\n      await writeFile(getReadmePath(sessionDir, dirName), readme, 'utf-8');\n\n      // Track review update\n      fulltextUpdates.set(reviewIndex, fulltextRef);\n    }\n\n    created++;\n    const entry: FulltextInitEntry = { dirName, citationKey, title: article.title };\n    if (article.doi) entry.doi = article.doi;\n    if (article.pmid) entry.pmid = article.pmid;\n    entries.push(entry);\n  }\n\n  if (!dryRun) {\n    // Ensure fulltext directory exists\n    await mkdir(getFulltextDir(sessionDir), { recursive: true });\n\n    // Update reviews.yaml with fulltext references\n    if (fulltextUpdates.size > 0) {\n      for (const [reviewIdx, ref] of fulltextUpdates) {\n        reviewFile.articles[reviewIdx]!.fulltext = ref;\n      }\n      await writeFile(reviewsPath, stringifyYaml(reviewFile), 'utf-8');\n    }\n  }\n\n  return {\n    created,\n    skipped,\n    entries,\n    ...(dryRun && { dryRun: true }),\n  };\n}\n"],"names":["parseYaml","stringifyYaml"],"mappings":";;;;;;;;AAoCA,eAAsB,oBACpB,SAC6B;AAC7B,QAAM,EAAE,WAAW,aAAa,OAAA,IAAW;AAC3C,QAAM,aAAa,KAAK,aAAa,SAAS;AAG9C,QAAM,cAAc,KAAK,YAAY,aAAa,cAAc;AAChE,QAAM,gBAAgB,MAAM,SAAS,aAAa,OAAO;AACzD,QAAM,aAAaA,MAAU,aAAa;AAG1C,QAAM,oBAAoB,WAAW,YAAY,CAAA,GAAI;AAAA,IACnD,CAAC,MAAM,EAAE,kBAAkB;AAAA,EAAA;AAI7B,QAAM,uCAAuB,IAAA;AAC7B,aAAW,WAAW,WAAW,YAAY,CAAA,GAAI;AAC/C,QAAI,QAAQ,UAAU,SAAS;AAC7B,uBAAiB,IAAI,QAAQ,SAAS,OAAO;AAAA,IAC/C;AAAA,EACF;AAEA,QAAM,UAA+B,CAAA;AACrC,QAAM,eAAyB,CAAA;AAC/B,MAAI,UAAU;AACd,MAAI,UAAU;AAGd,QAAM,sCAAsB,IAAA;AAE5B,WAAS,IAAI,GAAG,IAAI,iBAAiB,QAAQ,KAAK;AAChD,UAAM,UAAU,iBAAiB,CAAC;AAGlC,UAAM,cAAc,WAAW,SAAS,QAAQ,OAAO;AAGvD,QAAI,QAAQ,UAAU,WAAW,iBAAiB,IAAI,QAAQ,SAAS,OAAO,GAAG;AAC/E;AACA;AAAA,IACF;AAGA,UAAM,cAAc,oBAAoB,QAAQ,SAAS,QAAQ,MAAM,YAAY;AACnF,iBAAa,KAAK,WAAW;AAE7B,UAAM,OAAO,WAAA;AACb,UAAM,UAAU,gBAAgB,aAAa,IAAI;AAGjD,UAAM,WAA6C;AAAA,MACjD;AAAA,MACA;AAAA,MACA,OAAO,QAAQ;AAAA,IAAA;AAEjB,QAAI,QAAQ,IAAK,UAAS,MAAM,QAAQ;AACxC,QAAI,QAAQ,KAAM,UAAS,OAAO,QAAQ;AAC1C,QAAI,QAAQ,QAAS,UAAS,UAAU,QAAQ;AAChD,QAAI,QAAQ,QAAS,UAAS,UAAU,QAAQ;AAChD,QAAI,QAAQ,KAAM,UAAS,OAAO,QAAQ;AAC1C,UAAM,OAAO,WAAW,QAAQ;AAGhC,UAAM,cAAkC;AAAA,MACtC;AAAA,MACA,UAAU,EAAE,KAAK,OAAO,KAAK,OAAO,UAAU,MAAA;AAAA,IAAM;AAGtD,QAAI,CAAC,QAAQ;AAEX,YAAM,aAAa,cAAc,YAAY,OAAO;AACpD,YAAM,MAAM,YAAY,EAAE,WAAW,MAAM;AAG3C,YAAM,SAAS,YAAY,YAAY,OAAO,GAAG,IAAI;AAGrD,YAAM,SAAS,eAAe,IAAI;AAClC,YAAM,UAAU,cAAc,YAAY,OAAO,GAAG,QAAQ,OAAO;AAGnE,sBAAgB,IAAI,aAAa,WAAW;AAAA,IAC9C;AAEA;AACA,UAAM,QAA2B,EAAE,SAAS,aAAa,OAAO,QAAQ,MAAA;AACxE,QAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,QAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,YAAQ,KAAK,KAAK;AAAA,EACpB;AAEA,MAAI,CAAC,QAAQ;AAEX,UAAM,MAAM,eAAe,UAAU,GAAG,EAAE,WAAW,MAAM;AAG3D,QAAI,gBAAgB,OAAO,GAAG;AAC5B,iBAAW,CAAC,WAAW,GAAG,KAAK,iBAAiB;AAC9C,mBAAW,SAAS,SAAS,EAAG,WAAW;AAAA,MAC7C;AACA,YAAM,UAAU,aAAaC,UAAc,UAAU,GAAG,OAAO;AAAA,IACjE;AAAA,EACF;AAEA,SAAO;AAAA,IACL;AAAA,IACA;AAAA,IACA;AAAA,IACA,GAAI,UAAU,EAAE,QAAQ,KAAA;AAAA,EAAK;AAEjC;"}
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[]).filter(\n    (a) => a.finalDecision === 'include',\n  );\n\n  // Collect existing dirNames from reviews for skip detection\n  const existingDirNames = new Set<string>();\n  for (const article of reviewFile.articles ?? []) {\n    if (article.fulltext?.dirName) {\n      existingDirNames.add(article.fulltext.dirName);\n    }\n  }\n\n  const entries: FulltextInitEntry[] = [];\n  const existingKeys: string[] = [];\n  let created = 0;\n  let skipped = 0;\n\n  // Track which articles in reviewFile to update with fulltext refs\n  const fulltextUpdates = new Map<number, ArticleFulltextRef>();\n\n  for (let i = 0; i < includedArticles.length; i++) {\n    const article = includedArticles[i]!;\n\n    // Find the article's index in the full review file (including non-included)\n    const reviewIndex = reviewFile.articles.indexOf(article);\n\n    // Skip if already has a fulltext directory\n    if (article.fulltext?.dirName && existingDirNames.has(article.fulltext.dirName)) {\n      skipped++;\n      continue;\n    }\n\n    // Generate citation key and directory name\n    const citationKey = generateCitationKey(article.authors, article.year, existingKeys);\n    existingKeys.push(citationKey);\n\n    const uuid = randomUUID();\n    const dirName = generateDirName(citationKey, uuid);\n\n    // Create meta\n    const metaOpts: Parameters<typeof createMeta>[0] = {\n      citationKey,\n      uuid,\n      title: article.title,\n    };\n    if (article.doi) metaOpts.doi = article.doi;\n    if (article.pmid) metaOpts.pmid = article.pmid;\n    if (article.arxivId) metaOpts.arxivId = article.arxivId;\n    if (article.authors) metaOpts.authors = article.authors;\n    if (article.year) metaOpts.year = article.year;\n    const meta = createMeta(metaOpts);\n\n    // Build fulltext ref for reviews.yaml\n    const fulltextRef: ArticleFulltextRef = {\n      dirName,\n      hasFiles: { pdf: false, xml: false, html: false, markdown: false },\n    };\n\n    if (!dryRun) {\n      // Create directory\n      const articleDir = getArticleDir(sessionDir, dirName);\n      await mkdir(articleDir, { recursive: true });\n\n      // Write meta.json\n      await saveMeta(getMetaPath(sessionDir, dirName), meta);\n\n      // Write README.md\n      const readme = generateReadme(meta);\n      await writeFile(getReadmePath(sessionDir, dirName), readme, 'utf-8');\n\n      // Track review update\n      fulltextUpdates.set(reviewIndex, fulltextRef);\n    }\n\n    created++;\n    const entry: FulltextInitEntry = { dirName, citationKey, title: article.title };\n    if (article.doi) entry.doi = article.doi;\n    if (article.pmid) entry.pmid = article.pmid;\n    entries.push(entry);\n  }\n\n  if (!dryRun) {\n    // Ensure fulltext directory exists\n    await mkdir(getFulltextDir(sessionDir), { recursive: true });\n\n    // Update reviews.yaml with fulltext references\n    if (fulltextUpdates.size > 0) {\n      for (const [reviewIdx, ref] of fulltextUpdates) {\n        reviewFile.articles[reviewIdx]!.fulltext = ref;\n      }\n      await writeFile(reviewsPath, stringifyYaml(reviewFile), 'utf-8');\n    }\n  }\n\n  return {\n    created,\n    skipped,\n    entries,\n    ...(dryRun && { dryRun: true }),\n  };\n}\n"],"names":["parseYaml","stringifyYaml"],"mappings":";;;;;;;;;AAgCA,eAAsB,oBACpB,SAC6B;AAC7B,QAAM,EAAE,WAAW,aAAa,OAAA,IAAW;AAC3C,QAAM,aAAa,KAAK,aAAa,SAAS;AAG9C,QAAM,cAAc,KAAK,YAAY,aAAa,cAAc;AAChE,QAAM,gBAAgB,MAAM,SAAS,aAAa,OAAO;AACzD,QAAM,aAAaA,MAAU,aAAa;AAG1C,QAAM,oBAAoB,WAAW,YAAY,CAAA,GAAI;AAAA,IACnD,CAAC,MAAM,EAAE,kBAAkB;AAAA,EAAA;AAI7B,QAAM,uCAAuB,IAAA;AAC7B,aAAW,WAAW,WAAW,YAAY,CAAA,GAAI;AAC/C,QAAI,QAAQ,UAAU,SAAS;AAC7B,uBAAiB,IAAI,QAAQ,SAAS,OAAO;AAAA,IAC/C;AAAA,EACF;AAEA,QAAM,UAA+B,CAAA;AACrC,QAAM,eAAyB,CAAA;AAC/B,MAAI,UAAU;AACd,MAAI,UAAU;AAGd,QAAM,sCAAsB,IAAA;AAE5B,WAAS,IAAI,GAAG,IAAI,iBAAiB,QAAQ,KAAK;AAChD,UAAM,UAAU,iBAAiB,CAAC;AAGlC,UAAM,cAAc,WAAW,SAAS,QAAQ,OAAO;AAGvD,QAAI,QAAQ,UAAU,WAAW,iBAAiB,IAAI,QAAQ,SAAS,OAAO,GAAG;AAC/E;AACA;AAAA,IACF;AAGA,UAAM,cAAc,oBAAoB,QAAQ,SAAS,QAAQ,MAAM,YAAY;AACnF,iBAAa,KAAK,WAAW;AAE7B,UAAM,OAAO,WAAA;AACb,UAAM,UAAU,gBAAgB,aAAa,IAAI;AAGjD,UAAM,WAA6C;AAAA,MACjD;AAAA,MACA;AAAA,MACA,OAAO,QAAQ;AAAA,IAAA;AAEjB,QAAI,QAAQ,IAAK,UAAS,MAAM,QAAQ;AACxC,QAAI,QAAQ,KAAM,UAAS,OAAO,QAAQ;AAC1C,QAAI,QAAQ,QAAS,UAAS,UAAU,QAAQ;AAChD,QAAI,QAAQ,QAAS,UAAS,UAAU,QAAQ;AAChD,QAAI,QAAQ,KAAM,UAAS,OAAO,QAAQ;AAC1C,UAAM,OAAO,WAAW,QAAQ;AAGhC,UAAM,cAAkC;AAAA,MACtC;AAAA,MACA,UAAU,EAAE,KAAK,OAAO,KAAK,OAAO,MAAM,OAAO,UAAU,MAAA;AAAA,IAAM;AAGnE,QAAI,CAAC,QAAQ;AAEX,YAAM,aAAa,cAAc,YAAY,OAAO;AACpD,YAAM,MAAM,YAAY,EAAE,WAAW,MAAM;AAG3C,YAAM,SAAS,YAAY,YAAY,OAAO,GAAG,IAAI;AAGrD,YAAM,SAAS,eAAe,IAAI;AAClC,YAAM,UAAU,cAAc,YAAY,OAAO,GAAG,QAAQ,OAAO;AAGnE,sBAAgB,IAAI,aAAa,WAAW;AAAA,IAC9C;AAEA;AACA,UAAM,QAA2B,EAAE,SAAS,aAAa,OAAO,QAAQ,MAAA;AACxE,QAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,QAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,YAAQ,KAAK,KAAK;AAAA,EACpB;AAEA,MAAI,CAAC,QAAQ;AAEX,UAAM,MAAM,eAAe,UAAU,GAAG,EAAE,WAAW,MAAM;AAG3D,QAAI,gBAAgB,OAAO,GAAG;AAC5B,iBAAW,CAAC,WAAW,GAAG,KAAK,iBAAiB;AAC9C,mBAAW,SAAS,SAAS,EAAG,WAAW;AAAA,MAC7C;AACA,YAAM,UAAU,aAAaC,UAAc,UAAU,GAAG,OAAO;AAAA,IACjE;AAAA,EACF;AAEA,SAAO;AAAA,IACL;AAAA,IACA;AAAA,IACA;AAAA,IACA,GAAI,UAAU,EAAE,QAAQ,KAAA;AAAA,EAAK;AAEjC;"}

package/dist/cli/commands/fulltext/pending.d.ts

@@ -1,4 +1,4 @@
-import { OALocation } from '../../../fulltext/types.js';
+import { OALocation } from '@ncukondo/academic-fulltext';
 export interface FulltextPendingOptions {
     sessionDir: string;
     format?: 'table' | 'json';

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

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

@@ -1,8 +1,10 @@
 import { readFile, writeFile } from "node:fs/promises";
 import { join } from "node:path";
 import { parse } from "yaml";
-import { loadMeta } from "../../../fulltext/meta.js";
-import { getMetaPath } from "../../../fulltext/paths.js";
+import { loadMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import { getMetaPath } from "../../../node_modules/@ncukondo/academic-fulltext/dist/paths.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import "node:crypto";
 async function hasFulltextFiles(sessionDir, dirName) {
   try {
     const metaPath = getMetaPath(sessionDir, dirName);

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

@@ -1 +1 @@
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+{"version":3,"file":"pending.js","sources":["../../../../src/cli/commands/fulltext/pending.ts"],"sourcesContent":["/**\n * Fulltext pending command.\n * Lists articles needing manual download with URLs.\n */\n\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { loadMeta, getMetaPath, type OALocation } from '@ncukondo/academic-fulltext';\nimport type { ReviewFile, ArticleEntry } from '../review/types.js';\n\nexport interface FulltextPendingOptions {\n  sessionDir: string;\n  format?: 'table' | 'json';\n  exportPath?: string | undefined;\n}\n\nexport interface PendingArticle {\n  dirName?: string;\n  citationKey?: string;\n  title: string;\n  doi?: string;\n  pmid?: string;\n  publisherUrl?: string;\n  oaLocations?: OALocation[];\n}\n\nexport interface FulltextPendingResult {\n  totalPending: number;\n  articles: PendingArticle[];\n}\n\n/**\n * Check if an article has any fulltext files by reading its meta.json.\n */\nasync function hasFulltextFiles(\n  sessionDir: string,\n  dirName: string,\n): Promise<boolean> {\n  try {\n    const metaPath = getMetaPath(sessionDir, dirName);\n    const meta = await loadMeta(metaPath);\n    return (\n      meta.files.pdf !== undefined ||\n      meta.files.markdown !== undefined\n    );\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Build a PendingArticle from an ArticleEntry, enriched with meta.json data.\n */\nasync function buildPendingArticle(\n  article: ArticleEntry,\n  sessionDir: string,\n): Promise<PendingArticle> {\n  const pending: PendingArticle = {\n    title: article.title,\n  };\n\n  if (article.doi) {\n    pending.doi = article.doi;\n    pending.publisherUrl = `https://doi.org/${article.doi}`;\n  }\n  if (article.pmid) pending.pmid = article.pmid;\n\n  if (article.fulltext?.dirName) {\n    pending.dirName = article.fulltext.dirName;\n\n    // Try to load meta.json for OA locations and citation key\n    try {\n      const metaPath = getMetaPath(sessionDir, article.fulltext.dirName);\n      const meta = await loadMeta(metaPath);\n      pending.citationKey = meta.citationKey;\n      if (meta.oaLocations && meta.oaLocations.length > 0) {\n        pending.oaLocations = meta.oaLocations;\n      }\n    } catch {\n      // meta.json not readable — skip enrichment\n    }\n  }\n\n  return pending;\n}\n\n/**\n * Format the export file content for batch download.\n * Format: comment line with article identifier, followed by URL lines.\n */\nexport function formatExportFile(articles: PendingArticle[]): string {\n  const blocks: string[] = [];\n\n  for (const article of articles) {\n    const identifier = article.dirName ?? article.title;\n    const header = identifier === article.title\n      ? `# ${article.title}`\n      : `# ${identifier} - ${article.title}`;\n    const lines: string[] = [header];\n\n    // Publisher URL (DOI link) first\n    if (article.publisherUrl) {\n      lines.push(article.publisherUrl);\n    }\n\n    // OA location URLs\n    if (article.oaLocations) {\n      for (const loc of article.oaLocations) {\n        lines.push(loc.url);\n      }\n    }\n\n    blocks.push(lines.join('\\n'));\n  }\n\n  return blocks.join('\\n\\n') + '\\n';\n}\n\n/**\n * Execute the fulltext pending command.\n * Lists included articles that don't yet have fulltext files.\n */\nexport async function executeFulltextPending(\n  options: FulltextPendingOptions,\n): Promise<FulltextPendingResult> {\n  const { sessionDir, exportPath } = options;\n\n  // Load reviews.yaml\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(content) as ReviewFile;\n\n  // Filter to included articles\n  const included = (reviewFile.articles ?? 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package/dist/cli/commands/fulltext/status.d.ts.map

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

@@ -1,8 +1,10 @@
 import { readFile } from "node:fs/promises";
 import { join } from "node:path";
 import { parse } from "yaml";
-import { loadMeta } from "../../../fulltext/meta.js";
-import { getMetaPath } from "../../../fulltext/paths.js";
+import { loadMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import { getMetaPath } from "../../../node_modules/@ncukondo/academic-fulltext/dist/paths.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import "node:crypto";
 async function classifyArticle(article, sessionDir) {
   if (!article.fulltext?.dirName) {
     return "not-initialized";

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

@@ -1 +1 @@
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+{"version":3,"file":"status.js","sources":["../../../../src/cli/commands/fulltext/status.ts"],"sourcesContent":["/**\n * Fulltext status command.\n * Shows overall fulltext retrieval status for a session.\n */\n\nimport { readFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { loadMeta, getMetaPath } from '@ncukondo/academic-fulltext';\nimport type { ReviewFile, ArticleEntry } from '../review/types.js';\n\nexport interface FulltextStatusOptions {\n  sessionDir: string;\n  format?: 'table' | 'json';\n}\n\nexport interface FulltextStatusResult {\n  totalIncluded: number;\n  withFulltext: number;\n  pdfOnly: number;\n  markdownOnly: number;\n  both: number;\n  pending: number;\n  notInitialized: number;\n}\n\n/**\n * Classify an article's fulltext state by reading its meta.json.\n * Returns: 'pdf-only' | 'markdown-only' | 'both' | 'pending' | 'not-initialized'\n */\nasync function classifyArticle(\n  article: ArticleEntry,\n  sessionDir: string,\n): Promise<'pdf-only' | 'markdown-only' | 'both' | 'pending' | 'not-initialized'> {\n  if (!article.fulltext?.dirName) {\n    return 'not-initialized';\n  }\n\n  try {\n    const metaPath = getMetaPath(sessionDir, article.fulltext.dirName);\n    const meta = await loadMeta(metaPath);\n\n    const hasPdf = meta.files.pdf !== undefined;\n    const hasMd = meta.files.markdown !== undefined;\n\n    if (hasPdf && hasMd) return 'both';\n    if (hasPdf) return 'pdf-only';\n    if (hasMd) return 'markdown-only';\n    return 'pending';\n  } catch {\n    // Can't read meta.json — treat as pending since directory was assigned\n    return 'pending';\n  }\n}\n\n/**\n * Execute the fulltext status command.\n * Scans included articles and reports fulltext retrieval status.\n */\nexport async function executeFulltextStatus(\n  options: FulltextStatusOptions,\n): Promise<FulltextStatusResult> {\n  const { sessionDir } = options;\n\n  // Load reviews.yaml\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(content) as ReviewFile;\n\n  // Filter to included articles\n  const included = (reviewFile.articles ?? []).filter(\n    (a) => a.finalDecision === 'include',\n  );\n\n  const result: FulltextStatusResult = {\n    totalIncluded: included.length,\n    withFulltext: 0,\n    pdfOnly: 0,\n    markdownOnly: 0,\n    both: 0,\n    pending: 0,\n    notInitialized: 0,\n  };\n\n  for (const article of included) {\n    const state = await classifyArticle(article, sessionDir);\n    switch (state) {\n      case 'pdf-only':\n        result.pdfOnly++;\n        result.withFulltext++;\n        break;\n      case 'markdown-only':\n        result.markdownOnly++;\n        result.withFulltext++;\n        break;\n      case 'both':\n        result.both++;\n        result.withFulltext++;\n        break;\n      case 'pending':\n        result.pending++;\n        break;\n      case 'not-initialized':\n        result.notInitialized++;\n        break;\n    }\n  }\n\n  return result;\n}\n"],"names":["parseYaml"],"mappings":";;;;;;;AA8BA,eAAe,gBACb,SACA,YACgF;AAChF,MAAI,CAAC,QAAQ,UAAU,SAAS;AAC9B,WAAO;AAAA,EACT;AAEA,MAAI;AACF,UAAM,WAAW,YAAY,YAAY,QAAQ,SAAS,OAAO;AACjE,UAAM,OAAO,MAAM,SAAS,QAAQ;AAEpC,UAAM,SAAS,KAAK,MAAM,QAAQ;AAClC,UAAM,QAAQ,KAAK,MAAM,aAAa;AAEtC,QAAI,UAAU,MAAO,QAAO;AAC5B,QAAI,OAAQ,QAAO;AACnB,QAAI,MAAO,QAAO;AAClB,WAAO;AAAA,EACT,QAAQ;AAEN,WAAO;AAAA,EACT;AACF;AAMA,eAAsB,sBACpB,SAC+B;AAC/B,QAAM,EAAE,eAAe;AAGvB,QAAM,cAAc,KAAK,YAAY,aAAa,cAAc;AAChE,QAAM,UAAU,MAAM,SAAS,aAAa,OAAO;AACnD,QAAM,aAAaA,MAAU,OAAO;AAGpC,QAAM,YAAY,WAAW,YAAY,CAAA,GAAI;AAAA,IAC3C,CAAC,MAAM,EAAE,kBAAkB;AAAA,EAAA;AAG7B,QAAM,SAA+B;AAAA,IACnC,eAAe,SAAS;AAAA,IACxB,cAAc;AAAA,IACd,SAAS;AAAA,IACT,cAAc;AAAA,IACd,MAAM;AAAA,IACN,SAAS;AAAA,IACT,gBAAgB;AAAA,EAAA;AAGlB,aAAW,WAAW,UAAU;AAC9B,UAAM,QAAQ,MAAM,gBAAgB,SAAS,UAAU;AACvD,YAAQ,OAAA;AAAA,MACN,KAAK;AACH,eAAO;AACP,eAAO;AACP;AAAA,MACF,KAAK;AACH,eAAO;AACP,eAAO;AACP;AAAA,MACF,KAAK;AACH,eAAO;AACP,eAAO;AACP;AAAA,MACF,KAAK;AACH,eAAO;AACP;AAAA,MACF,KAAK;AACH,eAAO;AACP;AAAA,IAAA;AAAA,EAEN;AAEA,SAAO;AACT;"}

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

@@ -1 +1 @@
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+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/fulltext/sync.ts"],"names":[],"mappings":"AAAA;;GAEG;AAgBH,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,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,EAAE,CAAC;CACjB;AAED,MAAM,WAAW,kBAAkB;IACjC,uCAAuC;IACvC,MAAM,EAAE,MAAM,CAAC;IACf,iCAAiC;IACjC,eAAe,EAAE,MAAM,CAAC;IACxB,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,mBAAmB,GAC3B,OAAO,CAAC,kBAAkB,CAAC,CAqI7B"}

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

@@ -1,11 +1,14 @@
 import { join } from "node:path";
 import { readdir, stat, readFile, writeFile } from "node:fs/promises";
 import { parse, stringify } from "yaml";
-import { loadMeta, updateMetaFiles, saveMeta } from "../../../fulltext/meta.js";
-import { getFulltextDir } from "../../../fulltext/paths.js";
+import { loadMeta, updateMetaFiles, saveMeta } from "../../../node_modules/@ncukondo/academic-fulltext/dist/meta.js";
+import { getFulltextDir } from "../../../node_modules/@ncukondo/academic-fulltext/dist/paths.js";
+import "../../../node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js";
+import "node:crypto";
 const FULLTEXT_FILES = {
   "fulltext.pdf": "pdf",
   "fulltext.xml": "xml",
+  "fulltext.html": "html",
   "fulltext.md": "markdown"
 };
 async function executeFulltextSync(options) {
@@ -72,6 +75,7 @@ async function executeFulltextSync(options) {
         const hasFiles = {
           pdf: !!updatedMeta.files.pdf,
           xml: !!updatedMeta.files.xml,
+          html: !!updatedMeta.files.html,
           markdown: !!updatedMeta.files.markdown
         };
         hasFilesUpdates.set(dirName, hasFiles);