@ncukondo/search-hub 0.12.2 → 0.14.0

package/dist/cli/commands/diff.js

@@ -136,8 +136,8 @@ function compareBlocks(block1, block2, index, field) {
   const emptyTerms = { keywords: [], mesh: [], emtree: [], exclude: [] };
   const terms1 = block1 ?? emptyTerms;
   const terms2 = block2 ?? emptyTerms;
-  const added = setDiff(terms1.keywords, terms2.keywords);
-  const removed = setDiff(terms2.keywords, terms1.keywords);
+  const added = setDiff(terms1.keywords ?? [], terms2.keywords ?? []);
+  const removed = setDiff(terms2.keywords ?? [], terms1.keywords ?? []);
   const meshAdded = setDiff(terms1.mesh ?? [], terms2.mesh ?? []);
   const meshRemoved = setDiff(terms2.mesh ?? [], terms1.mesh ?? []);
   const emtreeAdded = setDiff(terms1.emtree ?? [], terms2.emtree ?? []);

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

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

@@ -1,3 +1,8 @@
+/**
+ * The YAML template string with comments preserved.
+ * This is a raw string (not generated by a YAML library) so comments are kept.
+ */
+export declare const QUERY_SCHEMA_FILENAME = "query.schema.json";
 /**
  * Generate the query template YAML string.
  *

package/dist/cli/commands/query/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/init.ts"],"names":[],"mappings":"AAyDA;;;;GAIG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAED;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CAAC,OAAO,EAAE;IAChD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC,CA4BjD"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/init.ts"],"names":[],"mappings":"AASA;;;GAGG;AACH,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AAiDzD;;;;GAIG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAED;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CAAC,OAAO,EAAE;IAChD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC,CAkCjD"}

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

@@ -1,5 +1,9 @@
 import { access, writeFile } from "node:fs/promises";
-const QUERY_TEMPLATE = `name: my_search
+import { join, dirname } from "node:path";
+import { generateQueryJSONSchema } from "../../../query/json-schema.js";
+const QUERY_SCHEMA_FILENAME = "query.schema.json";
+const QUERY_TEMPLATE = `# yaml-language-server: $schema=./${QUERY_SCHEMA_FILENAME}
+name: my_search
 description: ""
 
 query:
@@ -62,12 +66,16 @@ async function writeQueryTemplate(options) {
     }
   }
   await writeFile(options.output, template, "utf-8");
+  const schemaPath = join(dirname(options.output), QUERY_SCHEMA_FILENAME);
+  const jsonSchema = generateQueryJSONSchema();
+  await writeFile(schemaPath, JSON.stringify(jsonSchema, null, 2) + "\n", "utf-8");
   return {
     success: true,
     message: `Template written to ${options.output}`
   };
 }
 export {
+  QUERY_SCHEMA_FILENAME,
   generateQueryTemplate,
   writeQueryTemplate
 };

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

@@ -1 +1 @@
-{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access } from \"node:fs/promises\";\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# overrides:                 # Optional: database-specific settings\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     filters:\\n\" +\n  \"#       publication_types:\\n\" +\n  \"#         exclude:\\n\" +\n  \"#           - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n  return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * @param options - Output options\n * @param options.output - File path to write to (if omitted, returns template in message)\n * @param options.force - Whether to overwrite existing files\n * @returns Result with success status and message\n */\nexport async function writeQueryTemplate(options: {\n  output?: string;\n  force?: boolean;\n}): Promise<{ success: boolean; message: string }> {\n  const template = generateQueryTemplate();\n\n  if (!options.output) {\n    // No output file specified, return template as message\n    return { success: true, message: template };\n  }\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(options.output);\n      // File exists and force is not set\n      return {\n        success: false,\n        message: `File already exists: ${options.output}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Write to file\n  await fsWriteFile(options.output, template, \"utf-8\");\n  return {\n    success: true,\n    message: `Template written to ${options.output}`,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";AAYA,MAAM,iBACJ;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAiDK,SAAS,wBAAgC;AAC9C,SAAO;AACT;AAUA,eAAsB,mBAAmB,SAGU;AACjD,QAAM,WAAW,sBAAA;AAEjB,MAAI,CAAC,QAAQ,QAAQ;AAEnB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,QAAQ,MAAM;AAE3B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,QAAQ,MAAM;AAAA,MAAA;AAAA,IAEnD,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAMA,UAAY,QAAQ,QAAQ,UAAU,OAAO;AACnD,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,uBAAuB,QAAQ,MAAM;AAAA,EAAA;AAElD;"}
+{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\nimport { generateQueryJSONSchema } from \"../../../query/json-schema.js\";\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\nexport const QUERY_SCHEMA_FILENAME = \"query.schema.json\";\n\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  `# yaml-language-server: $schema=./${QUERY_SCHEMA_FILENAME}\\n` +\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# overrides:                 # Optional: database-specific settings\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     filters:\\n\" +\n  \"#       publication_types:\\n\" +\n  \"#         exclude:\\n\" +\n  \"#           - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n  return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * @param options - Output options\n * @param options.output - File path to write to (if omitted, returns template in message)\n * @param options.force - Whether to overwrite existing files\n * @returns Result with success status and message\n */\nexport async function writeQueryTemplate(options: {\n  output?: string;\n  force?: boolean;\n}): Promise<{ success: boolean; message: string }> {\n  const template = generateQueryTemplate();\n\n  if (!options.output) {\n    // No output file specified, return template as message\n    return { success: true, message: template };\n  }\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(options.output);\n      // File exists and force is not set\n      return {\n        success: false,\n        message: `File already exists: ${options.output}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Write to file\n  await fsWriteFile(options.output, template, \"utf-8\");\n\n  // Generate JSON Schema file alongside output\n  const schemaPath = join(dirname(options.output), QUERY_SCHEMA_FILENAME);\n  const jsonSchema = generateQueryJSONSchema();\n  await fsWriteFile(schemaPath, JSON.stringify(jsonSchema, null, 2) + \"\\n\", \"utf-8\");\n\n  return {\n    success: true,\n    message: `Template written to ${options.output}`,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";;;AAaO,MAAM,wBAAwB;AAGrC,MAAM,iBACJ,qCAAqC,qBAAqB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAkDrD,SAAS,wBAAgC;AAC9C,SAAO;AACT;AAUA,eAAsB,mBAAmB,SAGU;AACjD,QAAM,WAAW,sBAAA;AAEjB,MAAI,CAAC,QAAQ,QAAQ;AAEnB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,QAAQ,MAAM;AAE3B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,QAAQ,MAAM;AAAA,MAAA;AAAA,IAEnD,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAMA,UAAY,QAAQ,QAAQ,UAAU,OAAO;AAGnD,QAAM,aAAa,KAAK,QAAQ,QAAQ,MAAM,GAAG,qBAAqB;AACtE,QAAM,aAAa,wBAAA;AACnB,QAAMA,UAAY,YAAY,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEjF,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,uBAAuB,QAAQ,MAAM;AAAA,EAAA;AAElD;"}

package/dist/cli/commands/query/translate.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/query/translate.js

@@ -64,6 +64,11 @@ function formatTranslateResult(result, filePath) {
     for (const [provider, translation] of Object.entries(result.translations)) {
       lines.push(`[${provider.toUpperCase()}]`);
       lines.push(translation.native);
+      if (translation.warnings && translation.warnings.length > 0) {
+        for (const warning of translation.warnings) {
+          lines.push(`⚠ ${warning}`);
+        }
+      }
       lines.push("");
     }
   }

package/dist/cli/commands/query/translate.js.map

@@ -1 +1 @@
-{"version":3,"file":"translate.js","sources":["../../../../src/cli/commands/query/translate.ts"],"sourcesContent":["/**\n * Query translate command implementation.\n *\n * Translates a YAML query file to native database query syntax for each provider.\n */\nimport { readFile } from 'node:fs/promises';\nimport { parseQueryString } from '../../../query/index.js';\nimport type { TranslatedQuery, ProviderName } from '../../../providers/base/types.js';\nimport { translateQuery as translatePubmed } from '../../../providers/pubmed/translator.js';\nimport { translateQuery as translateEric } from '../../../providers/eric/translator.js';\nimport { translateQuery as translateArxiv } from '../../../providers/arxiv/translator.js';\nimport { translateQuery as translateScopus } from '../../../providers/scopus/translator.js';\n\n/**\n * Available translators by provider name.\n */\nconst translators: Record<\n  string,\n  (ast: Parameters<typeof translatePubmed>[0]) => TranslatedQuery\n> = {\n  pubmed: translatePubmed,\n  eric: translateEric,\n  arxiv: translateArxiv,\n  scopus: translateScopus,\n};\n\n/**\n * Default providers to translate for.\n */\nconst DEFAULT_PROVIDERS: ProviderName[] = ['pubmed', 'eric', 'arxiv', 'scopus'];\n\n/**\n * Options for translate command.\n */\nexport interface TranslateOptions {\n  /** Specific providers to translate for */\n  providers?: ProviderName[];\n}\n\n/**\n * Result of query translation.\n */\nexport interface TranslateResult {\n  /** Whether translation succeeded */\n  success: boolean;\n  /** Error message if failed */\n  error?: string;\n  /** Translations by provider name */\n  translations?: Record<string, TranslatedQuery>;\n}\n\n/**\n * Translate a query YAML file to native syntax for each provider.\n *\n * @param filePath - Path to the query file\n * @param options - Translation options\n * @returns Translation result\n */\nexport async function translateQueryCommand(\n  filePath: string,\n  options: TranslateOptions = {}\n): Promise<TranslateResult> {\n  // Read file\n  let content: string;\n  try {\n    content = await readFile(filePath, 'utf-8');\n  } catch (error) {\n    const message =\n      error instanceof Error ? error.message : 'Failed to read file';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n\n  // Parse and validate\n  let ast;\n  try {\n    ast = parseQueryString(content);\n  } catch (error) {\n    const message =\n      error instanceof Error ? error.message : 'Failed to parse query file';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n\n  // Determine which providers to translate for\n  const providers = options.providers ?? DEFAULT_PROVIDERS;\n\n  // Translate for each provider\n  const translations: Record<string, TranslatedQuery> = {};\n\n  for (const provider of providers) {\n    const translator = translators[provider];\n    if (translator) {\n      try {\n        translations[provider] = translator(ast);\n      } catch (error) {\n        const message =\n          error instanceof Error\n            ? error.message\n            : `Failed to translate for ${provider}`;\n        return {\n          success: false,\n          error: `${provider}: ${message}`,\n        };\n      }\n    }\n  }\n\n  return {\n    success: true,\n    translations,\n  };\n}\n\n/**\n * Format translation result for display.\n */\nexport function formatTranslateResult(\n  result: TranslateResult,\n  filePath: string\n): string {\n  if (!result.success) {\n    return `✗ Failed to translate: ${filePath}\\n  Error: ${result.error}`;\n  }\n\n  const lines = [`Translations for: ${filePath}`, ''];\n\n  if (result.translations) {\n    for (const [provider, translation] of Object.entries(result.translations)) {\n      lines.push(`[${provider.toUpperCase()}]`);\n      lines.push(translation.native);\n      lines.push('');\n    }\n  }\n\n  return lines.join('\\n');\n}\n"],"names":["translatePubmed","translateEric","translateArxiv","translateScopus"],"mappings":";;;;;;;AAgBA,MAAM,cAGF;AAAA,EACF,QAAQA;AAAAA,EACR,MAAMC;AAAAA,EACN,OAAOC;AAAAA,EACP,QAAQC;AACV;AAKA,MAAM,oBAAoC,CAAC,UAAU,QAAQ,SAAS,QAAQ;AA6B9E,eAAsB,sBACpB,UACA,UAA4B,IACF;AAE1B,MAAI;AACJ,MAAI;AACF,cAAU,MAAM,SAAS,UAAU,OAAO;AAAA,EAC5C,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,MAAI;AACJ,MAAI;AACF,UAAM,iBAAiB,OAAO;AAAA,EAChC,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,QAAM,YAAY,QAAQ,aAAa;AAGvC,QAAM,eAAgD,CAAA;AAEtD,aAAW,YAAY,WAAW;AAChC,UAAM,aAAa,YAAY,QAAQ;AACvC,QAAI,YAAY;AACd,UAAI;AACF,qBAAa,QAAQ,IAAI,WAAW,GAAG;AAAA,MACzC,SAAS,OAAO;AACd,cAAM,UACJ,iBAAiB,QACb,MAAM,UACN,2BAA2B,QAAQ;AACzC,eAAO;AAAA,UACL,SAAS;AAAA,UACT,OAAO,GAAG,QAAQ,KAAK,OAAO;AAAA,QAAA;AAAA,MAElC;AAAA,IACF;AAAA,EACF;AAEA,SAAO;AAAA,IACL,SAAS;AAAA,IACT;AAAA,EAAA;AAEJ;AAKO,SAAS,sBACd,QACA,UACQ;AACR,MAAI,CAAC,OAAO,SAAS;AACnB,WAAO,0BAA0B,QAAQ;AAAA,WAAc,OAAO,KAAK;AAAA,EACrE;AAEA,QAAM,QAAQ,CAAC,qBAAqB,QAAQ,IAAI,EAAE;AAElD,MAAI,OAAO,cAAc;AACvB,eAAW,CAAC,UAAU,WAAW,KAAK,OAAO,QAAQ,OAAO,YAAY,GAAG;AACzE,YAAM,KAAK,IAAI,SAAS,YAAA,CAAa,GAAG;AACxC,YAAM,KAAK,YAAY,MAAM;AAC7B,YAAM,KAAK,EAAE;AAAA,IACf;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}
+{"version":3,"file":"translate.js","sources":["../../../../src/cli/commands/query/translate.ts"],"sourcesContent":["/**\n * Query translate command implementation.\n *\n * Translates a YAML query file to native database query syntax for each provider.\n */\nimport { readFile } from 'node:fs/promises';\nimport { parseQueryString } from '../../../query/index.js';\nimport type { TranslatedQuery, ProviderName } from '../../../providers/base/types.js';\nimport { translateQuery as translatePubmed } from '../../../providers/pubmed/translator.js';\nimport { translateQuery as translateEric } from '../../../providers/eric/translator.js';\nimport { translateQuery as translateArxiv } from '../../../providers/arxiv/translator.js';\nimport { translateQuery as translateScopus } from '../../../providers/scopus/translator.js';\n\n/**\n * Available translators by provider name.\n */\nconst translators: Record<\n  string,\n  (ast: Parameters<typeof translatePubmed>[0]) => TranslatedQuery\n> = {\n  pubmed: translatePubmed,\n  eric: translateEric,\n  arxiv: translateArxiv,\n  scopus: translateScopus,\n};\n\n/**\n * Default providers to translate for.\n */\nconst DEFAULT_PROVIDERS: ProviderName[] = ['pubmed', 'eric', 'arxiv', 'scopus'];\n\n/**\n * Options for translate command.\n */\nexport interface TranslateOptions {\n  /** Specific providers to translate for */\n  providers?: ProviderName[];\n}\n\n/**\n * Result of query translation.\n */\nexport interface TranslateResult {\n  /** Whether translation succeeded */\n  success: boolean;\n  /** Error message if failed */\n  error?: string;\n  /** Translations by provider name */\n  translations?: Record<string, TranslatedQuery>;\n}\n\n/**\n * Translate a query YAML file to native syntax for each provider.\n *\n * @param filePath - Path to the query file\n * @param options - Translation options\n * @returns Translation result\n */\nexport async function translateQueryCommand(\n  filePath: string,\n  options: TranslateOptions = {}\n): Promise<TranslateResult> {\n  // Read file\n  let content: string;\n  try {\n    content = await readFile(filePath, 'utf-8');\n  } catch (error) {\n    const message =\n      error instanceof Error ? error.message : 'Failed to read file';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n\n  // Parse and validate\n  let ast;\n  try {\n    ast = parseQueryString(content);\n  } catch (error) {\n    const message =\n      error instanceof Error ? error.message : 'Failed to parse query file';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n\n  // Determine which providers to translate for\n  const providers = options.providers ?? DEFAULT_PROVIDERS;\n\n  // Translate for each provider\n  const translations: Record<string, TranslatedQuery> = {};\n\n  for (const provider of providers) {\n    const translator = translators[provider];\n    if (translator) {\n      try {\n        translations[provider] = translator(ast);\n      } catch (error) {\n        const message =\n          error instanceof Error\n            ? error.message\n            : `Failed to translate for ${provider}`;\n        return {\n          success: false,\n          error: `${provider}: ${message}`,\n        };\n      }\n    }\n  }\n\n  return {\n    success: true,\n    translations,\n  };\n}\n\n/**\n * Format translation result for display.\n */\nexport function formatTranslateResult(\n  result: TranslateResult,\n  filePath: string\n): string {\n  if (!result.success) {\n    return `✗ Failed to translate: ${filePath}\\n  Error: ${result.error}`;\n  }\n\n  const lines = [`Translations for: ${filePath}`, ''];\n\n  if (result.translations) {\n    for (const [provider, translation] of Object.entries(result.translations)) {\n      lines.push(`[${provider.toUpperCase()}]`);\n      lines.push(translation.native);\n      if (translation.warnings && translation.warnings.length > 0) {\n        for (const warning of translation.warnings) {\n          lines.push(`⚠ ${warning}`);\n        }\n      }\n      lines.push('');\n    }\n  }\n\n  return lines.join('\\n');\n}\n"],"names":["translatePubmed","translateEric","translateArxiv","translateScopus"],"mappings":";;;;;;;AAgBA,MAAM,cAGF;AAAA,EACF,QAAQA;AAAAA,EACR,MAAMC;AAAAA,EACN,OAAOC;AAAAA,EACP,QAAQC;AACV;AAKA,MAAM,oBAAoC,CAAC,UAAU,QAAQ,SAAS,QAAQ;AA6B9E,eAAsB,sBACpB,UACA,UAA4B,IACF;AAE1B,MAAI;AACJ,MAAI;AACF,cAAU,MAAM,SAAS,UAAU,OAAO;AAAA,EAC5C,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,MAAI;AACJ,MAAI;AACF,UAAM,iBAAiB,OAAO;AAAA,EAChC,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,QAAM,YAAY,QAAQ,aAAa;AAGvC,QAAM,eAAgD,CAAA;AAEtD,aAAW,YAAY,WAAW;AAChC,UAAM,aAAa,YAAY,QAAQ;AACvC,QAAI,YAAY;AACd,UAAI;AACF,qBAAa,QAAQ,IAAI,WAAW,GAAG;AAAA,MACzC,SAAS,OAAO;AACd,cAAM,UACJ,iBAAiB,QACb,MAAM,UACN,2BAA2B,QAAQ;AACzC,eAAO;AAAA,UACL,SAAS;AAAA,UACT,OAAO,GAAG,QAAQ,KAAK,OAAO;AAAA,QAAA;AAAA,MAElC;AAAA,IACF;AAAA,EACF;AAEA,SAAO;AAAA,IACL,SAAS;AAAA,IACT;AAAA,EAAA;AAEJ;AAKO,SAAS,sBACd,QACA,UACQ;AACR,MAAI,CAAC,OAAO,SAAS;AACnB,WAAO,0BAA0B,QAAQ;AAAA,WAAc,OAAO,KAAK;AAAA,EACrE;AAEA,QAAM,QAAQ,CAAC,qBAAqB,QAAQ,IAAI,EAAE;AAElD,MAAI,OAAO,cAAc;AACvB,eAAW,CAAC,UAAU,WAAW,KAAK,OAAO,QAAQ,OAAO,YAAY,GAAG;AACzE,YAAM,KAAK,IAAI,SAAS,YAAA,CAAa,GAAG;AACxC,YAAM,KAAK,YAAY,MAAM;AAC7B,UAAI,YAAY,YAAY,YAAY,SAAS,SAAS,GAAG;AAC3D,mBAAW,WAAW,YAAY,UAAU;AAC1C,gBAAM,KAAK,KAAK,OAAO,EAAE;AAAA,QAC3B;AAAA,MACF;AACA,YAAM,KAAK,EAAE;AAAA,IACf;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

package/dist/cli/commands/query/validate.d.ts

@@ -1,3 +1,5 @@
+import { MeSHLookupClient } from '../../../query/mesh-lookup.js';
+import { CountVocabValidator, VocabValidationResult } from '../../../query/vocab-validator.js';
 /**
  * Result of query validation.
  */
@@ -10,6 +12,8 @@ export interface ValidateResult {
     queryName?: string;
     /** Number of query blocks (if valid) */
     blockCount?: number;
+    /** Controlled vocabulary validation results (auto-checked by default) */
+    vocabResult?: VocabValidationResult;
 }
 /**
  * Validate a query YAML file.
@@ -17,9 +21,26 @@ export interface ValidateResult {
  * @param filePath - Path to the query file
  * @returns Validation result
  */
-export declare function validateQueryCommand(filePath: string): Promise<ValidateResult>;
+export declare function validateQueryCommand(filePath: string, options?: {
+    meshClient?: MeSHLookupClient;
+    noVocab?: boolean;
+    countValidators?: CountVocabValidator[];
+}): Promise<ValidateResult>;
 /**
  * Format validation result for display.
  */
 export declare function formatValidateResult(result: ValidateResult, filePath: string): string;
+/**
+ * Check if a validation result contains invalid controlled vocabulary terms.
+ */
+export declare function hasVocabErrors(result: ValidateResult): boolean;
+/**
+ * Detect whether a YAML file has a yaml-language-server $schema comment
+ * in its first 5 lines.
+ */
+export declare function detectSchemaLink(filePath: string): Promise<boolean>;
+/**
+ * Format controlled vocabulary validation results for display.
+ */
+export declare function formatVocabValidationOutput(result: VocabValidationResult): string;
 //# sourceMappingURL=validate.d.ts.map

package/dist/cli/commands/query/validate.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/validate.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEtE,OAAO,EAGL,KAAK,mBAAmB,EACxB,KAAK,qBAAqB,EAC3B,MAAM,mCAAmC,CAAC;AAE3C;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,mCAAmC;IACnC,OAAO,EAAE,OAAO,CAAC;IACjB,0CAA0C;IAC1C,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,4BAA4B;IAC5B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,wCAAwC;IACxC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,yEAAyE;IACzE,WAAW,CAAC,EAAE,qBAAqB,CAAC;CACrC;AAyCD;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IACR,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,eAAe,CAAC,EAAE,mBAAmB,EAAE,CAAC;CACzC,GACA,OAAO,CAAC,cAAc,CAAC,CA0BzB;AAED;;GAEG;AACH,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,cAAc,EACtB,QAAQ,EAAE,MAAM,GACf,MAAM,CAiBR;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,cAAc,GAAG,OAAO,CAE9D;AAED;;;GAGG;AACH,wBAAsB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAQzE;AAED;;GAEG;AACH,wBAAgB,2BAA2B,CACzC,MAAM,EAAE,qBAAqB,GAC5B,MAAM,CA6BR"}

package/dist/cli/commands/query/validate.js

@@ -1,49 +1,56 @@
 import { readFile } from "node:fs/promises";
 import { parseQueryString } from "../../../query/parser.js";
 import { ValidationError } from "../../../query/validator.js";
+import { extractControlledVocabTerms, validateControlledVocab } from "../../../query/vocab-validator.js";
 import { ZodError } from "zod";
-async function validateQueryCommand(filePath) {
+async function parseQueryFile(filePath) {
   let content;
   try {
     content = await readFile(filePath, "utf-8");
   } catch (error) {
     const message = error instanceof Error ? error.message : "Failed to read file";
-    return {
-      success: false,
-      errors: [message]
-    };
+    return { result: { success: false, errors: [message] } };
   }
   try {
     const ast = parseQueryString(content);
-    return {
-      success: true,
-      queryName: ast.name,
-      blockCount: ast.blocks.length
-    };
+    return { ast };
   } catch (error) {
     if (error instanceof ZodError) {
       const errors = error.issues.map((e) => {
         const path = e.path.join(".");
         return path ? `${path}: ${e.message}` : e.message;
       });
-      return {
-        success: false,
-        errors
-      };
+      return { result: { success: false, errors } };
     }
     if (error instanceof ValidationError) {
-      return {
-        success: false,
-        errors: [error.message]
-      };
+      return { result: { success: false, errors: [error.message] } };
     }
     const message = error instanceof Error ? error.message : "Unknown validation error";
-    return {
-      success: false,
-      errors: [message]
-    };
+    return { result: { success: false, errors: [message] } };
   }
 }
+async function validateQueryCommand(filePath, options) {
+  const parsed = await parseQueryFile(filePath);
+  if ("result" in parsed) {
+    return parsed.result;
+  }
+  const result = {
+    success: true,
+    queryName: parsed.ast.name,
+    blockCount: parsed.ast.blocks.length
+  };
+  if (options?.meshClient && !options.noVocab) {
+    const terms = extractControlledVocabTerms(parsed.ast);
+    if (terms.length > 0) {
+      result.vocabResult = await validateControlledVocab(
+        parsed.ast,
+        options.meshClient,
+        options.countValidators ? { countValidators: options.countValidators } : void 0
+      );
+    }
+  }
+  return result;
+}
 function formatValidateResult(result, filePath) {
   if (result.success) {
     const lines2 = [
@@ -61,8 +68,44 @@ function formatValidateResult(result, filePath) {
   }
   return lines.join("\n");
 }
+function hasVocabErrors(result) {
+  return (result.vocabResult?.invalid.length ?? 0) > 0;
+}
+async function detectSchemaLink(filePath) {
+  try {
+    const content = await readFile(filePath, "utf-8");
+    const lines = content.split("\n").slice(0, 5);
+    return lines.some((line) => /yaml-language-server.*\$schema=/.test(line));
+  } catch {
+    return false;
+  }
+}
+function formatVocabValidationOutput(result) {
+  if (result.valid.length === 0 && result.invalid.length === 0 && result.errors.length === 0) {
+    return "";
+  }
+  const lines = ["", "Controlled vocabulary:"];
+  for (const item of result.valid) {
+    lines.push(`  ✓ ${item.vocabulary}: "${item.term}"`);
+  }
+  for (const item of result.invalid) {
+    lines.push(`  ✗ ${item.vocabulary}: "${item.term}" — not found`);
+    if (item.suggestions && item.suggestions.length > 0) {
+      lines.push(
+        `    Did you mean: ${item.suggestions.map((s) => `"${s}"`).join(", ")}`
+      );
+    }
+  }
+  for (const item of result.errors) {
+    lines.push(`  ⚠ ${item.vocabulary}: "${item.term}" — ${item.error}`);
+  }
+  return lines.join("\n");
+}
 export {
+  detectSchemaLink,
   formatValidateResult,
+  formatVocabValidationOutput,
+  hasVocabErrors,
   validateQueryCommand
 };
 //# sourceMappingURL=validate.js.map

package/dist/cli/commands/query/validate.js.map

@@ -1 +1 @@
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error.message : 'Failed to read file';\n    return { result: { success: false, errors: [message] } };\n  }\n\n  try {\n    const ast = parseQueryString(content);\n    return { ast };\n  } catch (error) {\n    if (error instanceof ZodError) {\n      const errors = error.issues.map((e) => {\n        const path = e.path.join('.');\n        return path ? `${path}: ${e.message}` : e.message;\n      });\n      return { result: { success: false, errors } };\n    }\n\n    if (error instanceof ValidationError) {\n      return { result: { success: false, errors: [error.message] } };\n    }\n\n    const message =\n      error instanceof Error ? error.message : 'Unknown validation error';\n    return { result: { success: false, errors: [message] } };\n  }\n}\n\n/**\n * Validate a query YAML file.\n *\n * @param filePath - Path to the query file\n * @returns Validation result\n */\nexport async function validateQueryCommand(\n  filePath: string,\n  options?: {\n    meshClient?: MeSHLookupClient;\n    noVocab?: boolean;\n    countValidators?: CountVocabValidator[];\n  }\n): Promise<ValidateResult> {\n  const parsed = await parseQueryFile(filePath);\n\n  if ('result' in parsed) {\n    return parsed.result;\n  }\n\n  const result: ValidateResult = {\n    success: true,\n    queryName: parsed.ast.name,\n    blockCount: parsed.ast.blocks.length,\n  };\n\n  // Auto-validate vocab when controlled vocab terms exist\n  if (options?.meshClient && !options.noVocab) {\n    const terms = extractControlledVocabTerms(parsed.ast);\n    if (terms.length > 0) {\n      result.vocabResult = await validateControlledVocab(\n        parsed.ast,\n        options.meshClient,\n        options.countValidators ? { countValidators: options.countValidators } : undefined\n      );\n    }\n  }\n\n  return result;\n}\n\n/**\n * Format validation result for display.\n */\nexport function formatValidateResult(\n  result: ValidateResult,\n  filePath: string\n): string {\n  if (result.success) {\n    const lines = [\n      `✓ Valid query file: ${filePath}`,\n      `  Name: ${result.queryName}`,\n      `  Blocks: ${result.blockCount}`,\n    ];\n    return lines.join('\\n');\n  }\n\n  const lines = [`✗ Invalid query file: ${filePath}`, '', 'Errors:'];\n  if (result.errors) {\n    for (const error of result.errors) {\n      lines.push(`  - ${error}`);\n    }\n  }\n  return lines.join('\\n');\n}\n\n/**\n * Check if a validation result contains invalid controlled vocabulary terms.\n */\nexport function hasVocabErrors(result: ValidateResult): boolean {\n  return (result.vocabResult?.invalid.length ?? 0) > 0;\n}\n\n/**\n * Detect whether a YAML file has a yaml-language-server $schema comment\n * in its first 5 lines.\n */\nexport async function detectSchemaLink(filePath: string): Promise<boolean> {\n  try {\n    const content = await readFile(filePath, 'utf-8');\n    const lines = content.split('\\n').slice(0, 5);\n    return lines.some((line) => /yaml-language-server.*\\$schema=/.test(line));\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Format controlled vocabulary validation results for display.\n */\nexport function formatVocabValidationOutput(\n  result: VocabValidationResult\n): string {\n  if (\n    result.valid.length === 0 &&\n    result.invalid.length === 0 &&\n    result.errors.length === 0\n  ) {\n    return '';\n  }\n\n  const lines: string[] = ['', 'Controlled vocabulary:'];\n\n  for (const item of result.valid) {\n    lines.push(`  ✓ ${item.vocabulary}: \"${item.term}\"`);\n  }\n\n  for (const item of result.invalid) {\n    lines.push(`  ✗ ${item.vocabulary}: \"${item.term}\" — not found`);\n    if (item.suggestions && item.suggestions.length > 0) {\n      lines.push(\n        `    Did you mean: ${item.suggestions.map((s) => `\"${s}\"`).join(', ')}`\n      );\n    }\n  }\n\n  for (const item of result.errors) {\n    lines.push(`  ⚠ ${item.vocabulary}: \"${item.term}\" — ${item.error}`);\n  }\n\n  return lines.join('\\n');\n}\n"],"names":["lines"],"mappings":";;;;;AAuCA,eAAe,eACb,UACyD;AACzD,MAAI;AACJ,MAAI;AACF,cAAU,MAAM,SAAS,UAAU,OAAO;AAAA,EAC5C,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO,EAAE,QAAQ,EAAE,SAAS,OAAO,QAAQ,CAAC,OAAO,IAAE;AAAA,EACvD;AAEA,MAAI;AACF,UAAM,MAAM,iBAAiB,OAAO;AACpC,WAAO,EAAE,IAAA;AAAA,EACX,SAAS,OAAO;AACd,QAAI,iBAAiB,UAAU;AAC7B,YAAM,SAAS,MAAM,OAAO,IAAI,CAAC,MAAM;AACrC,cAAM,OAAO,EAAE,KAAK,KAAK,GAAG;AAC5B,eAAO,OAAO,GAAG,IAAI,KAAK,EAAE,OAAO,KAAK,EAAE;AAAA,MAC5C,CAAC;AACD,aAAO,EAAE,QAAQ,EAAE,SAAS,OAAO,SAAO;AAAA,IAC5C;AAEA,QAAI,iBAAiB,iBAAiB;AACpC,aAAO,EAAE,QAAQ,EAAE,SAAS,OAAO,QAAQ,CAAC,MAAM,OAAO,IAAE;AAAA,IAC7D;AAEA,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO,EAAE,QAAQ,EAAE,SAAS,OAAO,QAAQ,CAAC,OAAO,IAAE;AAAA,EACvD;AACF;AAQA,eAAsB,qBACpB,UACA,SAKyB;AACzB,QAAM,SAAS,MAAM,eAAe,QAAQ;AAE5C,MAAI,YAAY,QAAQ;AACtB,WAAO,OAAO;AAAA,EAChB;AAEA,QAAM,SAAyB;AAAA,IAC7B,SAAS;AAAA,IACT,WAAW,OAAO,IAAI;AAAA,IACtB,YAAY,OAAO,IAAI,OAAO;AAAA,EAAA;AAIhC,MAAI,SAAS,cAAc,CAAC,QAAQ,SAAS;AAC3C,UAAM,QAAQ,4BAA4B,OAAO,GAAG;AACpD,QAAI,MAAM,SAAS,GAAG;AACpB,aAAO,cAAc,MAAM;AAAA,QACzB,OAAO;AAAA,QACP,QAAQ;AAAA,QACR,QAAQ,kBAAkB,EAAE,iBAAiB,QAAQ,oBAAoB;AAAA,MAAA;AAAA,IAE7E;AAAA,EACF;AAEA,SAAO;AACT;AAKO,SAAS,qBACd,QACA,UACQ;AACR,MAAI,OAAO,SAAS;AAClB,UAAMA,SAAQ;AAAA,MACZ,uBAAuB,QAAQ;AAAA,MAC/B,WAAW,OAAO,SAAS;AAAA,MAC3B,aAAa,OAAO,UAAU;AAAA,IAAA;AAEhC,WAAOA,OAAM,KAAK,IAAI;AAAA,EACxB;AAEA,QAAM,QAAQ,CAAC,yBAAyB,QAAQ,IAAI,IAAI,SAAS;AACjE,MAAI,OAAO,QAAQ;AACjB,eAAW,SAAS,OAAO,QAAQ;AACjC,YAAM,KAAK,OAAO,KAAK,EAAE;AAAA,IAC3B;AAAA,EACF;AACA,SAAO,MAAM,KAAK,IAAI;AACxB;AAKO,SAAS,eAAe,QAAiC;AAC9D,UAAQ,OAAO,aAAa,QAAQ,UAAU,KAAK;AACrD;AAMA,eAAsB,iBAAiB,UAAoC;AACzE,MAAI;AACF,UAAM,UAAU,MAAM,SAAS,UAAU,OAAO;AAChD,UAAM,QAAQ,QAAQ,MAAM,IAAI,EAAE,MAAM,GAAG,CAAC;AAC5C,WAAO,MAAM,KAAK,CAAC,SAAS,kCAAkC,KAAK,IAAI,CAAC;AAAA,EAC1E,QAAQ;AACN,WAAO;AAAA,EACT;AACF;AAKO,SAAS,4BACd,QACQ;AACR,MACE,OAAO,MAAM,WAAW,KACxB,OAAO,QAAQ,WAAW,KAC1B,OAAO,OAAO,WAAW,GACzB;AACA,WAAO;AAAA,EACT;AAEA,QAAM,QAAkB,CAAC,IAAI,wBAAwB;AAErD,aAAW,QAAQ,OAAO,OAAO;AAC/B,UAAM,KAAK,OAAO,KAAK,UAAU,MAAM,KAAK,IAAI,GAAG;AAAA,EACrD;AAEA,aAAW,QAAQ,OAAO,SAAS;AACjC,UAAM,KAAK,OAAO,KAAK,UAAU,MAAM,KAAK,IAAI,eAAe;AAC/D,QAAI,KAAK,eAAe,KAAK,YAAY,SAAS,GAAG;AACnD,YAAM;AAAA,QACJ,qBAAqB,KAAK,YAAY,IAAI,CAAC,MAAM,IAAI,CAAC,GAAG,EAAE,KAAK,IAAI,CAAC;AAAA,MAAA;AAAA,IAEzE;AAAA,EACF;AAEA,aAAW,QAAQ,OAAO,QAAQ;AAChC,UAAM,KAAK,OAAO,KAAK,UAAU,MAAM,KAAK,IAAI,OAAO,KAAK,KAAK,EAAE;AAAA,EACrE;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

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

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

@@ -190,8 +190,7 @@ async function executeReviewExtract(options, sessionsDir) {
   const outputDir = dirname(outputPath);
   await mkdir(outputDir, { recursive: true });
   await writeFile(outputPath, finalContent, "utf-8");
-  const schemasDir = join(dirname(sessionsDir), ".search-hub", "schemas");
-  const schemaSourcePath = join(schemasDir, "review.schema.json");
+  const schemaSourcePath = join(sessionDir, ".internal", "review.schema.json");
   const schemaDestPath = join(outputDir, "review.schema.json");
   try {
     await access(schemaSourcePath);

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

@@ -1 +1 @@
-{"version":3,"file":"extract.js","sources":["../../../../src/cli/commands/review/extract.ts"],"sourcesContent":["/**\n * review extract command - Extract subset of articles for distributed review\n */\n\nimport { join, dirname } from 'node:path';\nimport { readFile, writeFile, mkdir, copyFile, access } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ArticleEntry, type ReviewStatus, type ReviewBasis } from './types.js';\n\nexport type SortOption = 'year' | 'title' | 'random' | 'none';\n\nexport interface ReviewExtractOptions {\n  sessionId: string;\n  filter?: ReviewStatus[];\n  sort?: SortOption;\n  seed?: number;\n  limit?: number;\n  offset?: number;\n  /** Basis for the review (title, abstract, fulltext). When specified, outputs screening format. */\n  basis?: ReviewBasis;\n  /** Reviewer identifier (e.g., \"ai:claude\"). Required for all extract modes. */\n  reviewer?: string;\n  /** Name for the review subset (output goes to for-review/<name>/review.yaml) */\n  name: string;\n  /** When true, outputs final decision format with reviewHistory and finalDecision fields. */\n  finalize?: boolean;\n}\n\n\nexport interface ReviewExtractResult {\n  outputPath: string;\n  extractedCount: number;\n  totalMatching: number;\n}\n\n/**\n * Load review file from session directory\n */\nasync function loadReviewFile(sessionDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Seeded random number generator (Fisher-Yates shuffle with LCG)\n */\nfunction seededShuffle<T>(array: T[], seed: number): T[] {\n  const result = [...array];\n  let currentSeed = seed;\n\n  // Linear congruential generator\n  function random(): number {\n    currentSeed = (currentSeed * 1664525 + 1013904223) % 4294967296;\n    return currentSeed / 4294967296;\n  }\n\n  // Fisher-Yates shuffle\n  for (let i = result.length - 1; i > 0; i--) {\n    const j = Math.floor(random() * (i + 1));\n    [result[i], result[j]] = [result[j]!, result[i]!];\n  }\n\n  return result;\n}\n\n/**\n * Get the best identifier for an article (doi > pmid > scopusId > arxivId > ericId > title)\n */\nfunction getArticleId(article: ArticleEntry): string {\n  if (article.doi) return article.doi;\n  if (article.pmid) return article.pmid;\n  if (article.scopusId) return article.scopusId;\n  if (article.arxivId) return article.arxivId;\n  if (article.ericId) return article.ericId;\n  return article.title;\n}\n\nfunction getBasisGuidanceComment(basis: ReviewBasis): string {\n  const schemaLine = '# yaml-language-server: $schema=./review.schema.json';\n  switch (basis) {\n    case 'title':\n      return [\n        schemaLine,\n        '# Screening by title only.',\n        '# Mark clearly irrelevant items as \"exclude\" with a comment explaining the reason.',\n        '# Leave everything else as \"uncertain\".',\n        '',\n      ].join('\\n');\n    case 'abstract':\n      return [\n        schemaLine,\n        '# Screening by title and abstract.',\n        '# You should be able to decide \"include\" or \"exclude\" for most items at this stage.',\n        '# Mark remaining ambiguous items as \"uncertain\" with a comment explaining why.',\n        '',\n      ].join('\\n');\n    case 'fulltext':\n      return [\n        schemaLine,\n        '# Screening by full text. This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\nfunction getDecisionInlineComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return '# exclude / uncertain';\n    case 'abstract':\n    case 'fulltext':\n      return '# include / exclude / uncertain';\n  }\n}\n\n/** Build a screening article for --basis mode: only include fields relevant to the basis */\nfunction buildScreeningArticle(article: ArticleEntry, basis: ReviewBasis): ArticleEntry {\n  // Start with identifiers\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Include abstract for abstract and fulltext basis\n  if ((basis === 'abstract' || basis === 'fulltext') && article.abstract) {\n    result.abstract = article.abstract;\n  }\n\n  // Include fulltext ref for fulltext basis\n  if (basis === 'fulltext' && article.fulltext) {\n    result.fulltext = article.fulltext;\n  }\n\n  // Pre-populate reviews (reviewer omitted; filled from top-level field on merge)\n  result.reviews = [{ decision: 'uncertain' as const, comment: '' } as ArticleEntry['reviews'][0]];\n\n  return result;\n}\n\n/** Build a finalize article with reviewHistory and finalDecision, optionally scoped by basis */\nfunction buildFinalizeArticle(article: ArticleEntry, basis?: ReviewBasis): ArticleEntry {\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n\n  // Always include identifiers\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Always include bibliographic metadata\n  if (article.authors) result.authors = article.authors;\n  if (article.year) result.year = article.year;\n\n  // Scope content by basis (or include all if no basis)\n  if (!basis || basis === 'abstract' || basis === 'fulltext') {\n    if (article.abstract) result.abstract = article.abstract;\n  }\n  if (!basis || basis === 'fulltext') {\n    if (article.fulltext) result.fulltext = article.fulltext;\n  }\n\n  // Add reviewHistory (existing reviews, read-only)\n  result.reviewHistory = article.reviews ?? [];\n\n  // Empty reviews for new reviews\n  result.reviews = [];\n\n  // Null finalDecision as placeholder\n  result.finalDecision = null;\n\n  return result;\n}\n\nfunction getFinalDecisionGuidanceComment(): string {\n  return [\n    '# yaml-language-server: $schema=./review.schema.json',\n    '# Final decision file: set finalDecision on each article',\n    '# Valid decisions: include / exclude / null',\n    '',\n  ].join('\\n');\n}\n\n/**\n * Sort articles based on sort option\n */\nfunction sortArticles(articles: ArticleEntry[], sort: SortOption, seed?: number): ArticleEntry[] {\n  switch (sort) {\n    case 'year':\n      return [...articles].sort((a, b) => {\n        const yearA = a.year ?? '';\n        const yearB = b.year ?? '';\n        return yearA.localeCompare(yearB);\n      });\n    case 'title':\n      return [...articles].sort((a, b) => a.title.localeCompare(b.title));\n    case 'random':\n      return seededShuffle(articles, seed ?? Date.now());\n    case 'none':\n    default:\n      return articles;\n  }\n}\n\n/**\n * Validate the name parameter for extract\n */\nexport function validateName(name: string): void {\n  if (!name || name.trim() === '') {\n    throw new Error('--name must not be empty');\n  }\n  if (name.includes('/') || name.includes('\\\\')) {\n    throw new Error(`--name must not contain path separators: \"${name}\"`);\n  }\n  if (name.includes('..')) {\n    throw new Error(`--name must not contain \"..\": \"${name}\"`);\n  }\n}\n\n/**\n * Execute review extract command\n */\nexport async function executeReviewExtract(\n  options: ReviewExtractOptions,\n  sessionsDir: string\n): Promise<ReviewExtractResult> {\n  validateName(options.name);\n\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const outputPath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n  const reviewFile = await loadReviewFile(sessionDir);\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 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yamlWithComments = yamlContent.replace(\n      /^(\\s*-?\\s*)decision: uncertain$/gm,\n      `$1decision: uncertain          ${decisionComment}`\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    const guidanceComment = getFinalDecisionGuidanceComment();\n    finalContent = guidanceComment + yamlWithComments;\n  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This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\nfunction getDecisionInlineComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return '# exclude / uncertain';\n    case 'abstract':\n    case 'fulltext':\n      return '# include / exclude / uncertain';\n  }\n}\n\n/** Build a screening article for --basis mode: only include fields relevant to the basis */\nfunction buildScreeningArticle(article: ArticleEntry, basis: ReviewBasis): ArticleEntry {\n  // Start with identifiers\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Include abstract for abstract and fulltext basis\n  if ((basis === 'abstract' || basis === 'fulltext') && article.abstract) {\n    result.abstract = article.abstract;\n  }\n\n  // Include fulltext ref for fulltext basis\n  if (basis === 'fulltext' && article.fulltext) {\n    result.fulltext = article.fulltext;\n  }\n\n  // Pre-populate reviews (reviewer omitted; filled from top-level field on merge)\n  result.reviews = [{ decision: 'uncertain' as const, comment: '' } as ArticleEntry['reviews'][0]];\n\n  return result;\n}\n\n/** Build a finalize article with reviewHistory and finalDecision, optionally scoped by basis */\nfunction buildFinalizeArticle(article: ArticleEntry, basis?: ReviewBasis): ArticleEntry {\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n\n  // Always include identifiers\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Always include bibliographic metadata\n  if (article.authors) result.authors = article.authors;\n  if (article.year) result.year = article.year;\n\n  // Scope content by basis (or include all if no basis)\n  if (!basis || basis === 'abstract' || basis === 'fulltext') {\n    if (article.abstract) result.abstract = article.abstract;\n  }\n  if (!basis || basis === 'fulltext') {\n    if (article.fulltext) result.fulltext = article.fulltext;\n  }\n\n  // Add reviewHistory (existing reviews, read-only)\n  result.reviewHistory = article.reviews ?? 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yamlWithComments = yamlContent.replace(\n      /^(\\s*-?\\s*)decision: uncertain$/gm,\n      `$1decision: uncertain          ${decisionComment}`\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    const guidanceComment = getFinalDecisionGuidanceComment();\n    finalContent = guidanceComment + yamlWithComments;\n  }\n\n  // Ensure output directory exists\n  const outputDir = dirname(outputPath);\n  await mkdir(outputDir, { recursive: true });\n\n  // Write output YAML\n  await writeFile(outputPath, finalContent, 'utf-8');\n\n  // Copy schema file to output directory if it exists\n  const schemaSourcePath = join(sessionDir, '.internal', 'review.schema.json');\n  const schemaDestPath = join(outputDir, 'review.schema.json');\n\n  try {\n    await access(schemaSourcePath);\n    await copyFile(schemaSourcePath, schemaDestPath);\n  } catch {\n    // Schema file doesn't exist, skip copying\n  }\n\n  return {\n    outputPath,\n    extractedCount: paginated.length,\n    totalMatching,\n  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package/dist/cli/commands/review/finalize.d.ts.map

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

@@ -48,8 +48,7 @@ async function executeReviewFinalize(options, sessionsDir) {
   }
   if (!options.dryRun) {
     const yamlContent = stringify(reviewFile, { 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
 `;
     await writeFile(reviewsPath, schemaComment + yamlContent, "utf-8");
   }

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

@@ -1 +1 @@
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