@ncukondo/search-hub 0.12.2 → 0.14.0

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

@@ -86,8 +86,7 @@ async function executeReviewInit(options, sessionsDir) {
     lineWidth: 0
     // Disable line wrapping
   });
-  const schemaPath = "../../../../.search-hub/schemas/review.schema.json";
-  const schemaComment = `# yaml-language-server: $schema=${schemaPath}
+  const schemaComment = `# yaml-language-server: $schema=./review.schema.json
 `;
   const reviewsExample = `reviews:
         # - reviewer: human:your-name
@@ -98,9 +97,7 @@ async function executeReviewInit(options, sessionsDir) {
     reviewsExample
   );
   await writeFile(reviewsPath, finalContent, "utf-8");
-  const schemasDir = join(dirname(sessionsDir), ".search-hub", "schemas");
-  await mkdir(schemasDir, { recursive: true });
-  const schemaDestPath = join(schemasDir, "review.schema.json");
+  const schemaDestPath = join(internalDir, "review.schema.json");
   try {
     const schemaSourcePath = await findSchemaSource();
     await copyFile(schemaSourcePath, schemaDestPath);

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

@@ -1 +1 @@
-{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/review/init.ts"],"sourcesContent":["/**\n * review init command - Generate reviews.yaml from session results\n */\n\nimport { join, dirname } from 'node:path';\nimport { writeFile, mkdir, access, copyFile } from 'node:fs/promises';\nimport { stringify as stringifyYaml } from 'yaml';\nimport type { Article, Author, ProviderName } from '../../../providers/base/types.js';\nimport { loadSession } from '../../../session/manager.js';\nimport { loadResults } from '../../../session/results-io.js';\nimport { deduplicateForReview } from './dedup.js';\nimport type { ArticleEntry, ReviewFile, MergedSource } from './types.js';\n\nexport interface ReviewInitOptions {\n  sessionId: string;\n  force?: boolean;\n}\n\nexport interface ReviewInitResult {\n  reviewsPath: string;\n  articleCount: number;\n  duplicatesRemoved: number;\n}\n\n/**\n * Format authors array to string\n */\nfunction formatAuthors(authors: Author[]): string {\n  return authors\n    .map((a) => {\n      const parts: string[] = [];\n      if (a.family) parts.push(a.family);\n      if (a.given) parts.push(a.given.charAt(0));\n      return parts.join(' ');\n    })\n    .join(', ');\n}\n\n/**\n * Extract year from publication date\n */\nfunction extractYear(publicationDate?: string): string | undefined {\n  if (!publicationDate) return undefined;\n  const year = publicationDate.substring(0, 4);\n  return /^\\d{4}$/.test(year) ? year : undefined;\n}\n\n/**\n * Convert Article to ArticleEntry for review file\n */\nfunction articleToEntry(article: Article & { mergedFrom?: MergedSource[] }): ArticleEntry {\n  const entry: ArticleEntry = {\n    title: article.title,\n    reviews: [],\n  };\n\n  // Add identifiers\n  if (article.doi) entry.doi = article.doi;\n  if (article.pmid) entry.pmid = article.pmid;\n  if (article.scopusId) entry.scopusId = article.scopusId;\n  if (article.arxivId) entry.arxivId = article.arxivId;\n  if (article.ericId) entry.ericId = article.ericId;\n\n  // Add bibliographic info\n  if (article.authors && article.authors.length > 0) {\n    entry.authors = formatAuthors(article.authors);\n  }\n  const year = extractYear(article.publicationDate);\n  if (year) entry.year = year;\n  if (article.abstract) entry.abstract = article.abstract;\n\n  // Add deduplication tracking\n  if (article.mergedFrom && article.mergedFrom.length > 0) {\n    entry.mergedFrom = article.mergedFrom;\n  }\n\n  return entry;\n}\n\n/**\n * Find the schema file location (in the package)\n */\nasync function findSchemaSource(): Promise<string> {\n  // Try relative to this file (src/cli/commands/review -> schemas)\n  const possiblePaths = [\n    join(dirname(import.meta.url.replace('file://', '')), '../../../../schemas/review.schema.json'),\n    join(process.cwd(), 'schemas/review.schema.json'),\n  ];\n\n  for (const path of possiblePaths) {\n    try {\n      await access(path);\n      return path;\n    } catch {\n      // Try next path\n    }\n  }\n\n  throw new Error('Could not find review.schema.json');\n}\n\n/**\n * Execute review init command\n */\nexport async function executeReviewInit(\n  options: ReviewInitOptions,\n  sessionsDir: string\n): Promise<ReviewInitResult> {\n  const sessionDir = join(sessionsDir, options.sessionId);\n\n  // Load session file\n  const session = await loadSession(options.sessionId, sessionsDir);\n\n  // Check if .internal/reviews.yaml already exists\n  const internalDir = join(sessionDir, '.internal');\n  const reviewsPath = join(internalDir, 'reviews.yaml');\n  try {\n    await access(reviewsPath);\n    if (!options.force) {\n      throw new Error(`reviews.yaml already exists. Use --force to overwrite.`);\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {\n      throw err;\n    }\n  }\n\n  // Create .internal/ directory\n  await mkdir(internalDir, { recursive: true });\n\n  // Load all results from session\n  const allArticles: Article[] = [];\n  const providers = Object.keys(session.databases) as ProviderName[];\n\n  for (const provider of providers) {\n    const dbStatus = session.databases[provider];\n    if (!dbStatus) continue;\n    const articles = await loadResults(sessionDir, provider);\n    allArticles.push(...articles);\n  }\n\n  // Deduplicate with mergedFrom tracking\n  const { articles: dedupedArticles, duplicatesRemoved } = deduplicateForReview(allArticles);\n\n  // Convert to ArticleEntry format\n  const articleEntries = dedupedArticles.map(articleToEntry);\n\n  // Build review file\n  const reviewFile: ReviewFile = {\n    sessionId: options.sessionId,\n    articles: articleEntries,\n  };\n\n  // Generate YAML with schema reference comment\n  const yamlContent = stringifyYaml(reviewFile, {\n    lineWidth: 0, // Disable line wrapping\n  });\n\n  // Add schema reference comment at top\n  // Path from sessions/{id}/.internal/ to .search-hub/schemas/\n  const schemaPath = '../../../../.search-hub/schemas/review.schema.json';\n  const schemaComment = `# yaml-language-server: $schema=${schemaPath}\\n`;\n\n  // Replace empty reviews arrays with commented example\n  const reviewsExample = `reviews:\n        # - reviewer: human:your-name\n        #   decision: include  # include / exclude / uncertain\n        #   comment: reason`;\n  const finalContent = schemaComment + yamlContent.replace(\n    /reviews: \\[\\]/g,\n    reviewsExample\n  );\n\n  // Write reviews.yaml\n  await writeFile(reviewsPath, finalContent, 'utf-8');\n\n  // Copy schema file to .search-hub/schemas/\n  const schemasDir = join(dirname(sessionsDir), '.search-hub', 'schemas');\n  await mkdir(schemasDir, { recursive: true });\n  const schemaDestPath = join(schemasDir, 'review.schema.json');\n\n  try {\n    const schemaSourcePath = await findSchemaSource();\n    await copyFile(schemaSourcePath, schemaDestPath);\n  } catch {\n    // If we can't find the schema file, skip copying\n    // This might happen in test environments\n  }\n\n  return {\n    reviewsPath,\n    articleCount: articleEntries.length,\n    duplicatesRemoved,\n  };\n}\n"],"names":["stringifyYaml"],"mappings":";;;;;;AA2BA,SAAS,cAAc,SAA2B;AAChD,SAAO,QACJ,IAAI,CAAC,MAAM;AACV,UAAM,QAAkB,CAAA;AACxB,QAAI,EAAE,OAAQ,OAAM,KAAK,EAAE,MAAM;AACjC,QAAI,EAAE,MAAO,OAAM,KAAK,EAAE,MAAM,OAAO,CAAC,CAAC;AACzC,WAAO,MAAM,KAAK,GAAG;AAAA,EACvB,CAAC,EACA,KAAK,IAAI;AACd;AAKA,SAAS,YAAY,iBAA8C;AACjE,MAAI,CAAC,gBAAiB,QAAO;AAC7B,QAAM,OAAO,gBAAgB,UAAU,GAAG,CAAC;AAC3C,SAAO,UAAU,KAAK,IAAI,IAAI,OAAO;AACvC;AAKA,SAAS,eAAe,SAAkE;AACxF,QAAM,QAAsB;AAAA,IAC1B,OAAO,QAAQ;AAAA,IACf,SAAS,CAAA;AAAA,EAAC;AAIZ,MAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,MAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAC/C,MAAI,QAAQ,QAAS,OAAM,UAAU,QAAQ;AAC7C,MAAI,QAAQ,OAAQ,OAAM,SAAS,QAAQ;AAG3C,MAAI,QAAQ,WAAW,QAAQ,QAAQ,SAAS,GAAG;AACjD,UAAM,UAAU,cAAc,QAAQ,OAAO;AAAA,EAC/C;AACA,QAAM,OAAO,YAAY,QAAQ,eAAe;AAChD,MAAI,YAAY,OAAO;AACvB,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAG/C,MAAI,QAAQ,cAAc,QAAQ,WAAW,SAAS,GAAG;AACvD,UAAM,aAAa,QAAQ;AAAA,EAC7B;AAEA,SAAO;AACT;AAKA,eAAe,mBAAoC;AAEjD,QAAM,gBAAgB;AAAA,IACpB,KAAK,QAAQ,YAAY,IAAI,QAAQ,WAAW,EAAE,CAAC,GAAG,wCAAwC;AAAA,IAC9F,KAAK,QAAQ,IAAA,GAAO,4BAA4B;AAAA,EAAA;AAGlD,aAAW,QAAQ,eAAe;AAChC,QAAI;AACF,YAAM,OAAO,IAAI;AACjB,aAAO;AAAA,IACT,QAAQ;AAAA,IAER;AAAA,EACF;AAEA,QAAM,IAAI,MAAM,mCAAmC;AACrD;AAKA,eAAsB,kBACpB,SACA,aAC2B;AAC3B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AAGtD,QAAM,UAAU,MAAM,YAAY,QAAQ,WAAW,WAAW;AAGhE,QAAM,cAAc,KAAK,YAAY,WAAW;AAChD,QAAM,cAAc,KAAK,aAAa,cAAc;AACpD,MAAI;AACF,UAAM,OAAO,WAAW;AACxB,QAAI,CAAC,QAAQ,OAAO;AAClB,YAAM,IAAI,MAAM,wDAAwD;AAAA,IAC1E;AAAA,EACF,SAAS,KAAK;AACZ,QAAK,IAA8B,SAAS,UAAU;AACpD,YAAM;AAAA,IACR;AAAA,EACF;AAGA,QAAM,MAAM,aAAa,EAAE,WAAW,MAAM;AAG5C,QAAM,cAAyB,CAAA;AAC/B,QAAM,YAAY,OAAO,KAAK,QAAQ,SAAS;AAE/C,aAAW,YAAY,WAAW;AAChC,UAAM,WAAW,QAAQ,UAAU,QAAQ;AAC3C,QAAI,CAAC,SAAU;AACf,UAAM,WAAW,MAAM,YAAY,YAAY,QAAQ;AACvD,gBAAY,KAAK,GAAG,QAAQ;AAAA,EAC9B;AAGA,QAAM,EAAE,UAAU,iBAAiB,kBAAA,IAAsB,qBAAqB,WAAW;AAGzF,QAAM,iBAAiB,gBAAgB,IAAI,cAAc;AAGzD,QAAM,aAAyB;AAAA,IAC7B,WAAW,QAAQ;AAAA,IACnB,UAAU;AAAA,EAAA;AAIZ,QAAM,cAAcA,UAAc,YAAY;AAAA,IAC5C,WAAW;AAAA;AAAA,EAAA,CACZ;AAID,QAAM,aAAa;AACnB,QAAM,gBAAgB,mCAAmC,UAAU;AAAA;AAGnE,QAAM,iBAAiB;AAAA;AAAA;AAAA;AAIvB,QAAM,eAAe,gBAAgB,YAAY;AAAA,IAC/C;AAAA,IACA;AAAA,EAAA;AAIF,QAAM,UAAU,aAAa,cAAc,OAAO;AAGlD,QAAM,aAAa,KAAK,QAAQ,WAAW,GAAG,eAAe,SAAS;AACtE,QAAM,MAAM,YAAY,EAAE,WAAW,MAAM;AAC3C,QAAM,iBAAiB,KAAK,YAAY,oBAAoB;AAE5D,MAAI;AACF,UAAM,mBAAmB,MAAM,iBAAA;AAC/B,UAAM,SAAS,kBAAkB,cAAc;AAAA,EACjD,QAAQ;AAAA,EAGR;AAEA,SAAO;AAAA,IACL;AAAA,IACA,cAAc,eAAe;AAAA,IAC7B;AAAA,EAAA;AAEJ;"}
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Use --force to overwrite.`);\n    }\n  } catch (err) {\n    if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {\n      throw err;\n    }\n  }\n\n  // Create .internal/ directory\n  await mkdir(internalDir, { recursive: true });\n\n  // Load all results from session\n  const allArticles: Article[] = [];\n  const providers = Object.keys(session.databases) as ProviderName[];\n\n  for (const provider of providers) {\n    const dbStatus = session.databases[provider];\n    if (!dbStatus) continue;\n    const articles = await loadResults(sessionDir, provider);\n    allArticles.push(...articles);\n  }\n\n  // Deduplicate with mergedFrom tracking\n  const { articles: dedupedArticles, duplicatesRemoved } = deduplicateForReview(allArticles);\n\n  // Convert to ArticleEntry format\n  const articleEntries = dedupedArticles.map(articleToEntry);\n\n  // Build review file\n  const reviewFile: ReviewFile = {\n    sessionId: options.sessionId,\n    articles: articleEntries,\n  };\n\n  // Generate YAML with schema reference comment\n  const yamlContent = stringifyYaml(reviewFile, {\n    lineWidth: 0, // Disable line wrapping\n  });\n\n  // Add schema reference comment at top (local copy alongside reviews.yaml)\n  const schemaComment = `# yaml-language-server: $schema=./review.schema.json\\n`;\n\n  // Replace empty reviews arrays with commented example\n  const reviewsExample = `reviews:\n        # - reviewer: human:your-name\n        #   decision: include  # include / exclude / uncertain\n        #   comment: reason`;\n  const finalContent = schemaComment + yamlContent.replace(\n    /reviews: \\[\\]/g,\n    reviewsExample\n  );\n\n  // Write reviews.yaml\n  await writeFile(reviewsPath, finalContent, 'utf-8');\n\n  // Copy schema file to .internal/ alongside reviews.yaml\n  const schemaDestPath = join(internalDir, 'review.schema.json');\n\n  try {\n    const schemaSourcePath = await findSchemaSource();\n    await copyFile(schemaSourcePath, schemaDestPath);\n  } catch {\n    // If we can't find the schema file, skip copying\n    // This might happen in test environments\n  }\n\n  return {\n    reviewsPath,\n    articleCount: articleEntries.length,\n    duplicatesRemoved,\n  };\n}\n"],"names":["stringifyYaml"],"mappings":";;;;;;AA2BA,SAAS,cAAc,SAA2B;AAChD,SAAO,QACJ,IAAI,CAAC,MAAM;AACV,UAAM,QAAkB,CAAA;AACxB,QAAI,EAAE,OAAQ,OAAM,KAAK,EAAE,MAAM;AACjC,QAAI,EAAE,MAAO,OAAM,KAAK,EAAE,MAAM,OAAO,CAAC,CAAC;AACzC,WAAO,MAAM,KAAK,GAAG;AAAA,EACvB,CAAC,EACA,KAAK,IAAI;AACd;AAKA,SAAS,YAAY,iBAA8C;AACjE,MAAI,CAAC,gBAAiB,QAAO;AAC7B,QAAM,OAAO,gBAAgB,UAAU,GAAG,CAAC;AAC3C,SAAO,UAAU,KAAK,IAAI,IAAI,OAAO;AACvC;AAKA,SAAS,eAAe,SAAkE;AACxF,QAAM,QAAsB;AAAA,IAC1B,OAAO,QAAQ;AAAA,IACf,SAAS,CAAA;AAAA,EAAC;AAIZ,MAAI,QAAQ,IAAK,OAAM,MAAM,QAAQ;AACrC,MAAI,QAAQ,KAAM,OAAM,OAAO,QAAQ;AACvC,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAC/C,MAAI,QAAQ,QAAS,OAAM,UAAU,QAAQ;AAC7C,MAAI,QAAQ,OAAQ,OAAM,SAAS,QAAQ;AAG3C,MAAI,QAAQ,WAAW,QAAQ,QAAQ,SAAS,GAAG;AACjD,UAAM,UAAU,cAAc,QAAQ,OAAO;AAAA,EAC/C;AACA,QAAM,OAAO,YAAY,QAAQ,eAAe;AAChD,MAAI,YAAY,OAAO;AACvB,MAAI,QAAQ,SAAU,OAAM,WAAW,QAAQ;AAG/C,MAAI,QAAQ,cAAc,QAAQ,WAAW,SAAS,GAAG;AACvD,UAAM,aAAa,QAAQ;AAAA,EAC7B;AAEA,SAAO;AACT;AAKA,eAAe,mBAAoC;AAEjD,QAAM,gBAAgB;AAAA,IACpB,KAAK,QAAQ,YAAY,IAAI,QAAQ,WAAW,EAAE,CAAC,GAAG,wCAAwC;AAAA,IAC9F,KAAK,QAAQ,IAAA,GAAO,4BAA4B;AAAA,EAAA;AAGlD,aAAW,QAAQ,eAAe;AAChC,QAAI;AACF,YAAM,OAAO,IAAI;AACjB,aAAO;AAAA,IACT,QAAQ;AAAA,IAER;AAAA,EACF;AAEA,QAAM,IAAI,MAAM,mCAAmC;AACrD;AAKA,eAAsB,kBACpB,SACA,aAC2B;AAC3B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AAGtD,QAAM,UAAU,MAAM,YAAY,QAAQ,WAAW,WAAW;AAGhE,QAAM,cAAc,KAAK,YAAY,WAAW;AAChD,QAAM,cAAc,KAAK,aAAa,cAAc;AACpD,MAAI;AACF,UAAM,OAAO,WAAW;AACxB,QAAI,CAAC,QAAQ,OAAO;AAClB,YAAM,IAAI,MAAM,wDAAwD;AAAA,IAC1E;AAAA,EACF,SAAS,KAAK;AACZ,QAAK,IAA8B,SAAS,UAAU;AACpD,YAAM;AAAA,IACR;AAAA,EACF;AAGA,QAAM,MAAM,aAAa,EAAE,WAAW,MAAM;AAG5C,QAAM,cAAyB,CAAA;AAC/B,QAAM,YAAY,OAAO,KAAK,QAAQ,SAAS;AAE/C,aAAW,YAAY,WAAW;AAChC,UAAM,WAAW,QAAQ,UAAU,QAAQ;AAC3C,QAAI,CAAC,SAAU;AACf,UAAM,WAAW,MAAM,YAAY,YAAY,QAAQ;AACvD,gBAAY,KAAK,GAAG,QAAQ;AAAA,EAC9B;AAGA,QAAM,EAAE,UAAU,iBAAiB,kBAAA,IAAsB,qBAAqB,WAAW;AAGzF,QAAM,iBAAiB,gBAAgB,IAAI,cAAc;AAGzD,QAAM,aAAyB;AAAA,IAC7B,WAAW,QAAQ;AAAA,IACnB,UAAU;AAAA,EAAA;AAIZ,QAAM,cAAcA,UAAc,YAAY;AAAA,IAC5C,WAAW;AAAA;AAAA,EAAA,CACZ;AAGD,QAAM,gBAAgB;AAAA;AAGtB,QAAM,iBAAiB;AAAA;AAAA;AAAA;AAIvB,QAAM,eAAe,gBAAgB,YAAY;AAAA,IAC/C;AAAA,IACA;AAAA,EAAA;AAIF,QAAM,UAAU,aAAa,cAAc,OAAO;AAGlD,QAAM,iBAAiB,KAAK,aAAa,oBAAoB;AAE7D,MAAI;AACF,UAAM,mBAAmB,MAAM,iBAAA;AAC/B,UAAM,SAAS,kBAAkB,cAAc;AAAA,EACjD,QAAQ;AAAA,EAGR;AAEA,SAAO;AAAA,IACL;AAAA,IACA,cAAc,eAAe;AAAA,IAC7B;AAAA,EAAA;AAEJ;"}

package/dist/cli/commands/review/merge.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"merge.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/review/merge.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,KAAK,EAAE,UAAU,EAAkC,WAAW,EAAE,MAAM,YAAY,CAAC;AA0B1F,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,2EAA2E;IAC3E,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,iBAAiB;IAChC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;IACvB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,0BAA0B,EAAE,MAAM,CAAC;IACnC,0BAA0B,EAAE,MAAM,CAAC;IACnC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAmBD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,UAAU,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAQ/F;AA8ND;;GAEG;AACH,wBAAsB,kBAAkB,CACtC,OAAO,EAAE,kBAAkB,EAC3B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,iBAAiB,CAAC,CAkC5B;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,iBAAiB,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAgDpF"}

package/dist/cli/commands/review/merge.js

@@ -194,8 +194,7 @@ async function executeReviewMerge(options, sessionsDir) {
     const yamlContent = stringify(mainFile, {
       lineWidth: 0
     });
-    const schemaPath = "../../../../.search-hub/schemas/review.schema.json";
-    const schemaComment = `# yaml-language-server: $schema=${schemaPath}
+    const schemaComment = `# yaml-language-server: $schema=./review.schema.json
 `;
     const finalContent = schemaComment + yamlContent;
     await writeFile(mainReviewsPath, finalContent, "utf-8");

package/dist/cli/commands/review/merge.js.map

@@ -1 +1 @@
-{"version":3,"file":"merge.js","sources":["../../../../src/cli/commands/review/merge.ts"],"sourcesContent":["/**\n * review merge command - Merge edited file back into main reviews.yaml\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, ArticleEntry, Review, WorkFile, ReviewBasis } from './types.js';\nimport { validateName } from './extract.js';\n\n\n/**\n * Check if a file is a work file (has basis field)\n */\n/** @deprecated Detects old WorkFile format (flat id/decision fields). Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('reviewer' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  // Distinguish from new ReviewFile-with-basis: old WorkFile has articles with flat `id` + `decision` fields\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: number;\n  finalDecisionsIncludeCount: number;\n  finalDecisionsExcludeCount: number;\n  warnings: string[];\n}\n\n/**\n * Load review file from path\n */\nasync function loadReviewFile(path: string): Promise<ReviewFile> {\n  const content = await readFile(path, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Auto-detect review basis from article data: fulltext > abstract > title\n */\nfunction detectBasis(article: ArticleEntry): ReviewBasis {\n  if (article.fulltext) return 'fulltext';\n  if (article.abstract) return 'abstract';\n  return 'title';\n}\n\n/**\n * Register a reviewer in the review file's reviewers registry.\n * Deduplicates by name+basis pair.\n */\nexport function registerReviewer(reviewFile: ReviewFile, name: string, basis: ReviewBasis): void {\n  if (!reviewFile.reviewers) {\n    reviewFile.reviewers = [];\n  }\n  const exists = reviewFile.reviewers.some((r) => r.name === name && r.basis === basis);\n  if (!exists) {\n    reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, ArxivId, EricId, or title\n */\nfunction findMatchingArticleById(\n  id: string,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  for (const main of mainArticles) {\n    // Match by DOI (case-insensitive)\n    if (main.doi && main.doi.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n    // Match by PMID\n    if (main.pmid && main.pmid === id) {\n      return main;\n    }\n    // Match by ScopusId\n    if (main.scopusId && main.scopusId === id) {\n      return main;\n    }\n    // Match by ArxivId\n    if (main.arxivId && main.arxivId === id) {\n      return main;\n    }\n    // Match by EricId\n    if (main.ericId && main.ericId === id) {\n      return main;\n    }\n    // Match by title (fallback, case-insensitive)\n    if (main.title.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Process work file format (with basis/reviewer)\n */\nfunction processWorkFile(\n  workFile: WorkFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    includeCount: 0,\n    excludeCount: 0,\n    uncertainCount: 0,\n    finalDecisionsSet: 0,\n    finalDecisionsIncludeCount: 0,\n    finalDecisionsExcludeCount: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n\n  // Register the reviewer for this work file's basis\n  if (!options.dryRun) {\n    registerReviewer(mainFile, workFile.reviewer, workFile.basis);\n  }\n\n  for (const workArticle of workFile.articles) {\n    // Skip articles with null decision (not yet reviewed)\n    if (workArticle.decision === null) {\n      continue;\n    }\n\n    const mainArticle = findMatchingArticleById(workArticle.id, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: id=\"${workArticle.id}\"`);\n      continue;\n    }\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    // Create review from work file article\n    const review: Review = {\n      reviewer: workFile.reviewer,\n      decision: workArticle.decision,\n      basis: workFile.basis,\n      timestamp,\n    };\n\n    // Add comment if provided\n    if (workArticle.comment) {\n      review.comment = workArticle.comment;\n    }\n\n    if (!options.dryRun) {\n      mainArticle.reviews.push(review);\n    }\n    result.reviewsAdded++;\n\n    // Count decision types\n    if (workArticle.decision === 'include') result.includeCount++;\n    else if (workArticle.decision === 'exclude') result.excludeCount++;\n    else if (workArticle.decision === 'uncertain') result.uncertainCount++;\n  }\n\n  return result;\n}\n\n/**\n * Process review file format (with reviewHistory separation)\n */\nfunction processReviewFile(\n  extractedFile: ReviewFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    includeCount: 0,\n    excludeCount: 0,\n    uncertainCount: 0,\n    finalDecisionsSet: 0,\n    finalDecisionsIncludeCount: 0,\n    finalDecisionsExcludeCount: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n  const topLevelReviewer = extractedFile.reviewer;\n\n  for (const extracted of extractedFile.articles) {\n    const mainArticle = findMatchingArticle(extracted, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: \"${extracted.title}\"`);\n      continue;\n    }\n\n    // Merge only reviews[] (reviewHistory is ignored)\n    const extractedReviews = extracted.reviews ?? [];\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    for (const review of extractedReviews) {\n      // Fill in reviewer from top-level field if not on individual review\n      const reviewer = review.reviewer ?? topLevelReviewer;\n      if (!reviewer) {\n        throw new Error('reviewer is required: set reviewer on individual review or top-level ReviewFile');\n      }\n      // Fill in basis from review, top-level field, or auto-detect from article data\n      const basis = review.basis ?? extractedFile.basis ?? detectBasis(extracted);\n\n      if (!options.dryRun) {\n        const mergedReview: Review = {\n          ...review,\n          reviewer,\n          basis,\n          timestamp: review.timestamp ?? timestamp,\n        };\n        mainArticle.reviews.push(mergedReview);\n\n        // Register reviewer\n        registerReviewer(mainFile, reviewer, basis);\n      }\n      result.reviewsAdded++;\n\n      // Count decision types\n      if (review.decision === 'include') result.includeCount++;\n      else if (review.decision === 'exclude') result.excludeCount++;\n      else if (review.decision === 'uncertain') result.uncertainCount++;\n    }\n\n    // Overwrite finalDecision if set in extracted (null means unset)\n    if (extracted.finalDecision !== undefined && extracted.finalDecision !== null) {\n      if (!options.dryRun) {\n        mainArticle.finalDecision = extracted.finalDecision;\n      }\n      result.decisionsSet++;\n      result.finalDecisionsSet++;\n      if (extracted.finalDecision === 'include') result.finalDecisionsIncludeCount++;\n      else if (extracted.finalDecision === 'exclude') result.finalDecisionsExcludeCount++;\n    }\n  }\n\n  return result;\n}\n\n/**\n * Execute review merge command\n */\nexport async function executeReviewMerge(\n  options: ReviewMergeOptions,\n  sessionsDir: string\n): Promise<ReviewMergeResult> {\n  validateName(options.name);\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const mainReviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const filePath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n\n  // Load both files\n  const mainFile = await loadReviewFile(mainReviewsPath);\n  const content = await readFile(filePath, 'utf-8');\n  const inputFile = parseYaml(content);\n\n  let result: ReviewMergeResult;\n\n  // Detect file format and process accordingly\n  if (isWorkFile(inputFile)) {\n    result = processWorkFile(inputFile, mainFile, options);\n  } else {\n    result = processReviewFile(inputFile as ReviewFile, mainFile, options);\n  }\n\n  // Write back if not dry-run\n  if (!options.dryRun) {\n    const yamlContent = stringifyYaml(mainFile, {\n      lineWidth: 0,\n    });\n\n    // Preserve schema reference comment\n    // Path from sessions/{id}/.internal/ to .search-hub/schemas/\n    const schemaPath = '../../../../.search-hub/schemas/review.schema.json';\n    const schemaComment = `# yaml-language-server: $schema=${schemaPath}\\n`;\n    const finalContent = schemaComment + yamlContent;\n\n    await writeFile(mainReviewsPath, finalContent, 'utf-8');\n  }\n\n  return result;\n}\n\n/**\n * Format merge result as human-readable string\n */\nexport function formatMergeOutput(result: ReviewMergeResult, dryRun: boolean): string {\n  const lines: string[] = [];\n\n  if (dryRun) {\n    lines.push('Dry run - no changes made');\n    lines.push('');\n  }\n\n  lines.push('Merge Summary:');\n\n  // Build reviews line with decision breakdown\n  if (result.reviewsAdded === 0) {\n    lines.push(`  Reviews added: 0`);\n  } else {\n    const parts: string[] = [];\n    if (result.excludeCount > 0) parts.push(`${result.excludeCount} exclude`);\n    if (result.includeCount > 0) parts.push(`${result.includeCount} include`);\n    if (result.uncertainCount > 0) parts.push(`${result.uncertainCount} uncertain`);\n\n    if (parts.length > 0) {\n      lines.push(`  Reviews added: ${result.reviewsAdded} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Reviews added: ${result.reviewsAdded}`);\n    }\n  }\n\n  // Show final decisions only when some were set\n  if (result.finalDecisionsSet > 0) {\n    const parts: string[] = [];\n    if (result.finalDecisionsIncludeCount > 0) parts.push(`${result.finalDecisionsIncludeCount} include`);\n    if (result.finalDecisionsExcludeCount > 0) parts.push(`${result.finalDecisionsExcludeCount} exclude`);\n\n    if (parts.length > 0) {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet}`);\n    }\n  }\n\n  if (result.warnings.length > 0) {\n    lines.push('');\n    lines.push('Warnings:');\n    for (const warning of result.warnings) {\n      lines.push(`  - ${warning}`);\n    }\n  }\n\n  return 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Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('reviewer' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  // Distinguish from new ReviewFile-with-basis: old WorkFile has articles with flat `id` + `decision` fields\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: 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reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, 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schemaComment + yamlContent;\n\n    await writeFile(mainReviewsPath, finalContent, 'utf-8');\n  }\n\n  return result;\n}\n\n/**\n * Format merge result as human-readable string\n */\nexport function formatMergeOutput(result: ReviewMergeResult, dryRun: boolean): string {\n  const lines: string[] = [];\n\n  if (dryRun) {\n    lines.push('Dry run - no changes made');\n    lines.push('');\n  }\n\n  lines.push('Merge Summary:');\n\n  // Build reviews line with decision breakdown\n  if (result.reviewsAdded === 0) {\n    lines.push(`  Reviews added: 0`);\n  } else {\n    const parts: string[] = [];\n    if (result.excludeCount > 0) parts.push(`${result.excludeCount} exclude`);\n    if (result.includeCount > 0) parts.push(`${result.includeCount} include`);\n    if (result.uncertainCount > 0) parts.push(`${result.uncertainCount} uncertain`);\n\n    if (parts.length > 0) {\n      lines.push(`  Reviews added: ${result.reviewsAdded} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Reviews added: ${result.reviewsAdded}`);\n    }\n  }\n\n  // Show final decisions only when some were set\n  if (result.finalDecisionsSet > 0) {\n    const parts: string[] = [];\n    if (result.finalDecisionsIncludeCount > 0) parts.push(`${result.finalDecisionsIncludeCount} include`);\n    if (result.finalDecisionsExcludeCount > 0) parts.push(`${result.finalDecisionsExcludeCount} exclude`);\n\n    if (parts.length > 0) {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet} (${parts.join(', ')})`);\n    } else {\n      lines.push(`  Final decisions set: ${result.finalDecisionsSet}`);\n    }\n  }\n\n  if (result.warnings.length > 0) {\n    lines.push('');\n    lines.push('Warnings:');\n    for (const warning of result.warnings) {\n      lines.push(`  - ${warning}`);\n    }\n  }\n\n  return 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package/dist/cli/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqKpC;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CA0tEvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiLpC;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CAkzEvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}

package/dist/cli/index.js

@@ -9,12 +9,16 @@ import "../config/schema.js";
 import { getDefaultConfig } from "../config/defaults.js";
 import { getDefaultConfigPath } from "../config/paths.js";
 import { viewConfig, viewConfigKey, setConfigKey } from "./commands/config.js";
-import { validateQueryCommand, formatValidateResult } from "./commands/query/validate.js";
+import { detectSchemaLink, validateQueryCommand, formatValidateResult, formatVocabValidationOutput, hasVocabErrors } from "./commands/query/validate.js";
+import { MeSHLookupClient } from "../query/mesh-lookup.js";
+import { RateLimiter } from "../providers/base/rate-limiter.js";
+import { VocabCache } from "../query/vocab-cache.js";
+import { createEricCountValidator, createEmtreeCountValidator } from "../query/vocab-validator.js";
+import { createProviderInstance, executePreview, executeCountOnly, executeSearch } from "./commands/search-executor.js";
 import { translateQueryCommand, formatTranslateResult } from "./commands/query/translate.js";
 import { writeQueryTemplate, generateQueryTemplate } from "./commands/query/init.js";
 import { getSessionDetails, computeDeduplicationStats, formatSessionDetails, listSessionsForDisplay, formatSessionList } from "./commands/status.js";
 import { parseSearchOptions, validateSearchInput, formatShortKeywordWarning, formatDryRunOutput, formatPreviewOutput, formatCountOnlyOutput } from "./commands/search.js";
-import { executePreview, executeCountOnly, executeSearch } from "./commands/search-executor.js";
 import { parseResumeOptions, validateResumeInput, getResumableProvidersForCommand } from "./commands/resume.js";
 import { executeResume } from "./commands/resume-executor.js";
 import { formatVerboseProviderDetails } from "./commands/search-utils.js";
@@ -172,16 +176,86 @@ Query YAML format (minimal):
       operator: OR
 
 Use "search-hub query init" to generate a template.`);
-  queryCommand.command("validate").description("Validate query YAML file").argument("<file>", "path to query YAML file").addHelpText("after", `
+  queryCommand.command("validate").description("Validate query YAML file (auto-checks controlled vocabulary)").argument("<file>", "path to query YAML file").option("--no-vocab", "skip controlled vocabulary validation").option("--no-cache", "skip vocabulary lookup cache").addHelpText("after", `
 Examples:
-  $ search-hub query validate ./diabetes-ai.yaml`).action(async (file) => {
+  $ search-hub query validate ./diabetes-ai.yaml
+  $ search-hub query validate ./diabetes-ai.yaml --no-vocab   # Skip MeSH check
+  $ search-hub query validate ./diabetes-ai.yaml --no-cache   # Ignore cache`).action(async (file, opts) => {
     const globalOpts = program.opts();
     try {
-      const result = await validateQueryCommand(file);
+      const noVocab = opts.vocab === false;
+      const noCache = opts.cache === false;
+      let cache;
+      if (!noVocab && !noCache) {
+        cache = new VocabCache();
+        await cache.load();
+      }
+      const hasSchema = await detectSchemaLink(file);
+      if (noVocab) {
+        const result2 = await validateQueryCommand(file, { noVocab });
+        if (!globalOpts.quiet) {
+          let output = formatValidateResult(result2, file);
+          const suggestion = formatSuggestion(getSuggestion({
+            command: "query validate",
+            queryFile: file,
+            validationSuccess: result2.success,
+            hasSchemaLink: hasSchema
+          }));
+          if (suggestion) output += "\n" + suggestion;
+          console.log(output);
+        }
+        process.exitCode = !result2.success ? EXIT_CODES.QUERY_ERROR : EXIT_CODES.SUCCESS;
+        return;
+      }
+      const rateLimiter = new RateLimiter({ tokensPerSecond: 3 });
+      const meshClient = new MeSHLookupClient({
+        rateLimiter,
+        ...cache ? { cache } : {}
+      });
+      const countValidators = [];
+      let config2;
+      try {
+        config2 = await loadConfig(
+          globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}
+        );
+      } catch {
+      }
+      if (config2) {
+        const ericProvider = createProviderInstance("eric", config2);
+        if (ericProvider) {
+          countValidators.push(
+            createEricCountValidator(ericProvider, cache ? { cache } : void 0)
+          );
+        }
+        const scopusProvider = createProviderInstance("scopus", config2);
+        if (scopusProvider) {
+          countValidators.push(
+            createEmtreeCountValidator(scopusProvider, cache ? { cache } : void 0)
+          );
+        }
+      }
+      const result = await validateQueryCommand(file, {
+        meshClient,
+        ...countValidators.length > 0 ? { countValidators } : {}
+      });
+      if (cache) {
+        await cache.save();
+      }
       if (!globalOpts.quiet) {
-        console.log(formatValidateResult(result, file));
+        let output = formatValidateResult(result, file);
+        if (result.vocabResult) {
+          output += formatVocabValidationOutput(result.vocabResult);
+        }
+        const suggestion = formatSuggestion(getSuggestion({
+          command: "query validate",
+          queryFile: file,
+          validationSuccess: result.success && !hasVocabErrors(result),
+          hasSchemaLink: hasSchema
+        }));
+        if (suggestion) output += "\n" + suggestion;
+        console.log(output);
       }
-      process.exitCode = result.success ? EXIT_CODES.SUCCESS : EXIT_CODES.QUERY_ERROR;
+      process.exitCode = !result.success || hasVocabErrors(result) ? EXIT_CODES.QUERY_ERROR : EXIT_CODES.SUCCESS;
     } catch (error) {
       if (!globalOpts.quiet) {
         console.error(