@ncukondo/search-hub 0.13.0 → 0.15.0

package/dist/cli/commands/search-executor.js.map

@@ -1 +1 @@
-{"version":3,"file":"search-executor.js","sources":["../../../src/cli/commands/search-executor.ts"],"sourcesContent":["/**\n * Search executor for CLI search command.\n *\n * Handles the actual execution of searches across multiple providers,\n * including session creation, progress display, and result storage.\n */\nimport { readFile, writeFile, appendFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { createHash } from 'node:crypto';\nimport type { SearchCommandOptions, CountResult, PreviewResult } from './search.js';\nimport type { Config } from '../../config/index.js';\nimport type {\n  Article,\n  Provider,\n  ProviderName,\n  TranslatedQuery,\n} from '../../providers/base/types.js';\nimport { isProviderError } from '../../providers/base/types.js';\nimport type { QueryAST } from '../../query/types.js';\nimport { parseQueryString } from '../../query/index.js';\nimport {\n  createSession,\n  updateDatabaseStatus,\n  updateSessionStatus,\n} from '../../session/manager.js';\nimport { MultiProviderProgress } from '../utils/progress.js';\nimport { PubMedProvider } from '../../providers/pubmed/provider.js';\nimport type { PubMedConfig } from '../../providers/pubmed/types.js';\nimport { ERICProvider } from '../../providers/eric/provider.js';\nimport { ArxivProvider } from '../../providers/arxiv/provider.js';\nimport { ScopusProvider } from '../../providers/scopus/provider.js';\nimport type { ScopusConfig } from '../../providers/scopus/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';\nimport { stringify as stringifyYaml } from 'yaml';\nimport { registerArticles, saveRegistrationRecord } from '../../integration/register.js';\nimport { buildFailureErrorMessage, buildPartialErrorMessage } from './search-utils.js';\nimport { getConfigDir } from '../../config/paths.js';\nimport type { RegistrationRecord } from '../../integration/types.js';\nimport { checkRefAvailable } from '../../integration/ref-cli.js';\nimport { convertResultsToYaml, loadResults } from '../../session/results-io.js';\n\n/**\n * Result of a search execution.\n */\nexport interface SearchExecutionResult {\n  success: boolean;\n  sessionId?: string;\n  results?: Record<string, { hits: number; retrieved: number; error?: string; warnings?: string[] }>;\n  error?: string;\n  autoRegisterResult?: RegistrationRecord;\n  sessionStatus: 'completed' | 'partial' | 'failed';\n}\n\n/**\n * Available providers that are implemented.\n */\nconst IMPLEMENTED_PROVIDERS: ProviderName[] = ['pubmed', 'eric', 'arxiv', 'scopus'];\n\n/**\n * Check if a provider has the required configuration (e.g., API keys).\n * Providers that require no special configuration always return true.\n */\nexport function isProviderConfigured(name: ProviderName, config: Config): boolean {\n  switch (name) {\n    case 'scopus':\n      return !!config.providers.scopus.api_key;\n    default:\n      return true; // pubmed, eric, arxiv require no API key\n  }\n}\n\n/**\n * Create a provider instance for the given provider name.\n */\nexport function createProviderInstance(\n  name: ProviderName,\n  config: Config\n): Provider | null {\n  const providerConfig = config.providers[name];\n\n  switch (name) {\n    case 'pubmed': {\n      if (!providerConfig.email) {\n        const configPath = getConfigDir();\n        console.warn(\n          `Warning: No email configured for PubMed.\\n` +\n          `  → Edit ${configPath}/config.toml and set providers.pubmed.email\\n` +\n          `  → Or run: search-hub config providers.pubmed.email \"your@email.com\"`\n        );\n      }\n      const pubmedOpts: PubMedConfig = {\n        email: providerConfig.email ?? 'search-hub@example.com',\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      };\n      if (providerConfig.api_key) {\n        pubmedOpts.apiKey = providerConfig.api_key;\n      }\n      return new PubMedProvider(pubmedOpts);\n    }\n    case 'eric':\n      return new ERICProvider({\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      });\n    case 'arxiv':\n      return new ArxivProvider({\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      });\n    case 'scopus': {\n      if (!providerConfig.api_key) {\n        console.warn(\n          `Warning: Scopus requires an API key. Set providers.scopus.api_key in config.\\n` +\n          `  → Get an API key at https://dev.elsevier.com/\\n` +\n          `  → Run: search-hub config providers.scopus.api_key \"your-key\"`\n        );\n        return null;\n      }\n      const scopusOpts: ScopusConfig = {\n        apiKey: providerConfig.api_key,\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      };\n      if (providerConfig.inst_token) {\n        scopusOpts.instToken = providerConfig.inst_token;\n      }\n      return new ScopusProvider(scopusOpts);\n    }\n    default:\n      throw new Error(`Provider '${name}' is not implemented`);\n  }\n}\n\n/**\n * Translate a query AST for a specific provider.\n */\nfunction translateQueryForProvider(\n  ast: QueryAST,\n  provider: ProviderName\n): TranslatedQuery {\n  switch (provider) {\n    case 'pubmed':\n      return translatePubmed(ast);\n    case 'eric':\n      return translateEric(ast);\n    case 'arxiv':\n      return translateArxiv(ast);\n    case 'scopus':\n      return translateScopus(ast);\n    default:\n      throw new Error(`No translator for provider '${provider}'`);\n  }\n}\n\n/**\n * Get enabled providers from config, optionally filtered by user selection.\n */\nfunction getEnabledProviders(\n  config: Config,\n  requestedProviders?: ProviderName[]\n): ProviderName[] {\n  const enabledInConfig = IMPLEMENTED_PROVIDERS.filter(\n    (name) => config.providers[name].enabled\n  );\n\n  if (requestedProviders && requestedProviders.length > 0) {\n    return requestedProviders.filter((p) => enabledInConfig.includes(p));\n  }\n\n  return enabledInConfig;\n}\n\n/**\n * Execute a search across multiple providers.\n */\nexport async function executeSearch(\n  options: SearchCommandOptions,\n  sessionsDir: string,\n  config: Config,\n  showProgress = true\n): Promise<SearchExecutionResult> {\n  let ast: QueryAST | undefined;\n  let queryContent: string;\n  let queryFile: string;\n\n  // Handle direct query mode\n  if (options.directQuery && options.providers && options.providers.length === 1) {\n    queryFile = 'direct-query';\n\n    // For direct query, we create a minimal AST structure\n    ast = {\n      name: options.sessionName ?? 'direct-query',\n      blocks: [\n        {\n          field: 'all',\n          terms: { keywords: [options.directQuery] },\n          operator: 'AND',\n        },\n      ],\n      filters: {},\n      overrides: {},\n    };\n\n    // Generate YAML safely using yaml library to handle special characters\n    queryContent = stringifyYaml({\n      name: ast.name,\n      blocks: ast.blocks,\n      filters: ast.filters,\n    });\n  } else if (options.queryFile) {\n    // Parse query file\n    try {\n      queryContent = await readFile(options.queryFile, 'utf-8');\n      ast = parseQueryString(queryContent);\n      queryFile = options.queryFile;\n    } catch (error) {\n      return {\n        success: false,\n        sessionStatus: 'failed',\n        error: `Failed to parse query file: ${error instanceof Error ? error.message : error}`,\n      };\n    }\n  } else {\n    return {\n      success: false,\n      sessionStatus: 'failed',\n      error: 'Either queryFile or directQuery with provider is required',\n    };\n  }\n\n  // Determine which providers to use\n  let providers = getEnabledProviders(config, options.providers);\n\n  // In default mode (no --db), skip unconfigured providers with a warning\n  const isExplicitSelection = options.providers && options.providers.length > 0;\n  if (!isExplicitSelection) {\n    const skipped: ProviderName[] = [];\n    providers = providers.filter((name) => {\n      if (!isProviderConfigured(name, config)) {\n        skipped.push(name);\n        return false;\n      }\n      return true;\n    });\n    for (const name of skipped) {\n      console.warn(\n        `Skipping ${name}: API key not configured (use --db ${name} to force)`\n      );\n    }\n  }\n\n  if (providers.length === 0) {\n    return {\n      success: false,\n      sessionStatus: 'failed',\n      error: 'No providers enabled or selected',\n    };\n  }\n\n  // Create query hash\n  const queryHash = createHash('sha256').update(queryContent).digest('hex').slice(0, 8);\n\n  // Create session\n  let session;\n  try {\n    const sessionOpts: Parameters<typeof createSession>[0] = {\n      name: options.sessionName ?? ast.name,\n      queryFile,\n      queryContent,\n      queryHash,\n      targets: providers,\n      sessionsDir,\n    };\n    if (ast.description) {\n      sessionOpts.description = ast.description;\n    }\n    session = await createSession(sessionOpts);\n  } catch (error) {\n    return {\n      success: false,\n      sessionStatus: 'failed',\n      error: `Failed to create session: ${error instanceof Error ? error.message : error}`,\n    };\n  }\n\n  const sessionId = session.id;\n  const results: Record<string, { hits: number; retrieved: number; error?: string; warnings?: string[] }> = {};\n\n  // Create progress display if enabled\n  let progress: MultiProviderProgress | undefined;\n  if (showProgress && process.stdout.isTTY) {\n    progress = new MultiProviderProgress(providers);\n  }\n\n  // Execute search for each provider\n  for (const providerName of providers) {\n    try {\n      // Create provider instance\n      const provider = createProviderInstance(providerName, config);\n\n      // Skip provider if it could not be created (e.g. missing configuration)\n      if (provider === null) {\n        const configError = `${providerName}: provider configuration incomplete. See warning above for details.`;\n        results[providerName] = { hits: 0, retrieved: 0, error: configError };\n        await updateDatabaseStatus(\n          sessionId,\n          providerName,\n          {\n            status: 'failed',\n            completedAt: new Date().toISOString(),\n            error: {\n              code: 'CONFIG_ERROR',\n              message: configError,\n              retryable: false,\n            },\n          },\n          sessionsDir\n        );\n        continue;\n      }\n\n      // Translate query\n      let translatedQuery: TranslatedQuery;\n      if (options.directQuery && options.providers?.length === 1) {\n        // For direct query, use the native query string directly\n        translatedQuery = {\n          native: options.directQuery,\n          provider: providerName,\n        };\n      } else {\n        translatedQuery = translateQueryForProvider(ast, providerName);\n      }\n\n      // Write translated query to session\n      const queryPath = join(sessionsDir, sessionId, `${providerName}_query.txt`);\n      await writeFile(queryPath, translatedQuery.native, 'utf-8');\n\n      // Update database status to in_progress\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'in_progress',\n          startedAt: new Date().toISOString(),\n        },\n        sessionsDir\n      );\n\n      // Prepare results file path\n      const resultsPath = join(sessionsDir, sessionId, `${providerName}_results.jsonl`);\n\n      // Execute search\n      let retrievedCount = 0;\n      let totalHits = 0;\n\n      progress?.update(providerName, 0, 0, 'in_progress');\n\n      const searchOptions = {\n        maxResults: options.maxResults ?? config.providers[providerName].max_results,\n      };\n\n      for await (const article of provider.search(translatedQuery, searchOptions)) {\n        retrievedCount++;\n\n        // Write article to JSONL file\n        await appendFile(resultsPath, JSON.stringify(article) + '\\n', 'utf-8');\n\n        // Update progress (estimate total from first batch)\n        if (totalHits === 0) {\n          // Estimate total - this is provider-dependent, we'll use retrieved count as minimum\n          totalHits = Math.max(retrievedCount * 10, 100);\n        }\n        progress?.update(providerName, retrievedCount, totalHits, 'in_progress');\n      }\n\n      // Update final totals\n      totalHits = retrievedCount; // Use actual count as final total\n\n      // Mark as completed\n      progress?.complete(providerName);\n\n      // Convert JSONL to YAML for human-readable view\n      const yamlFilename = `${providerName}_results.yaml`;\n      const yamlPath = join(sessionsDir, sessionId, yamlFilename);\n      await convertResultsToYaml(resultsPath, yamlPath, {\n        provider: providerName,\n        queryName: ast.name,\n      });\n\n      // Update database status\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'completed',\n          completedAt: new Date().toISOString(),\n          totalHits,\n          retrievedCount,\n          files: {\n            query: `${providerName}_query.txt`,\n            results: `${providerName}_results.jsonl`,\n            resultsYaml: yamlFilename,\n          },\n        },\n        sessionsDir\n      );\n\n      // Collect warnings if provider supports them\n      const providerWarnings = 'getWarnings' in provider && typeof (provider as any).getWarnings === 'function'\n        ? (provider as any).getWarnings() as string[]\n        : undefined;\n      results[providerName] = { hits: totalHits, retrieved: retrievedCount, ...(providerWarnings && providerWarnings.length > 0 && { warnings: providerWarnings }) };\n    } catch (error) {\n      const errorMessage = error instanceof Error\n          ? error.message\n          : isProviderError(error)\n            ? error.message\n            : String(error);\n\n      progress?.fail(providerName, errorMessage);\n\n      // Update database status with error\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'failed',\n          completedAt: new Date().toISOString(),\n          error: {\n            code: 'SEARCH_ERROR',\n            message: errorMessage,\n            retryable: true,\n          },\n        },\n        sessionsDir\n      );\n\n      results[providerName] = { hits: 0, retrieved: 0, error: errorMessage };\n    }\n  }\n\n  // Stop progress display\n  progress?.stop();\n\n  // Determine overall session status\n  const anyFailed = providers.some((p) => {\n    const r = results[p];\n    return r && r.error !== undefined;\n  });\n  const anySucceeded = providers.some((p) => {\n    const r = results[p];\n    return r && r.retrieved > 0;\n  });\n\n  let sessionStatus: 'completed' | 'partial' | 'failed';\n  if (!anyFailed) {\n    sessionStatus = 'completed';\n  } else if (anySucceeded) {\n    sessionStatus = 'partial';\n  } else {\n    sessionStatus = 'failed';\n  }\n\n  // Update session status\n  await updateSessionStatus(sessionId, sessionStatus, sessionsDir);\n\n  if (sessionStatus === 'failed') {\n    return {\n      success: false,\n      sessionId,\n      sessionStatus,\n      results,\n      error: buildFailureErrorMessage(results),\n    };\n  }\n\n  // In strict mode, partial success is treated as failure\n  if (options.strict && sessionStatus === 'partial') {\n    return {\n      success: false,\n      sessionId,\n      sessionStatus,\n      results,\n      error: buildPartialErrorMessage(results),\n    };\n  }\n\n  // Auto-register if enabled\n  let autoRegisterResult: RegistrationRecord | undefined;\n  if (\n    config.integration.reference_manager.enabled &&\n    config.integration.reference_manager.auto_register\n  ) {\n    const refAvailable = await checkRefAvailable();\n    if (refAvailable) {\n      // Load all articles from results files\n      const allArticles = await loadArticlesFromSession(sessionsDir, sessionId, providers);\n\n      if (allArticles.length > 0) {\n        autoRegisterResult = await registerArticles(allArticles, {\n          sessionId,\n          sessionDir: join(sessionsDir, sessionId),\n          withAbstracts: config.integration.reference_manager.with_abstracts,\n        });\n\n        // Save registration record\n        await saveRegistrationRecord(join(sessionsDir, sessionId), autoRegisterResult);\n      }\n    }\n  }\n\n  const result: SearchExecutionResult = {\n    success: true,\n    sessionId,\n    results,\n    sessionStatus,\n  };\n\n  if (autoRegisterResult) {\n    result.autoRegisterResult = autoRegisterResult;\n  }\n\n  return result;\n}\n\n/**\n * Execute count-only mode: get hit counts from each provider without downloading results.\n * No session is created.\n */\nexport async function executeCountOnly(\n  options: SearchCommandOptions,\n  config: Config\n): Promise<CountResult[]> {\n  let ast: QueryAST | undefined;\n\n  // Handle direct query mode\n  if (options.directQuery && options.providers && options.providers.length === 1) {\n    ast = {\n      name: options.sessionName ?? 'direct-query',\n      blocks: [\n        {\n          field: 'all',\n          terms: { keywords: [options.directQuery] },\n          operator: 'AND',\n        },\n      ],\n      filters: {},\n      overrides: {},\n    };\n  } else if (options.queryFile) {\n    const queryContent = await readFile(options.queryFile, 'utf-8');\n    ast = parseQueryString(queryContent);\n  } else {\n    return [];\n  }\n\n  // Determine which providers to use\n  let providers = getEnabledProviders(config, options.providers);\n\n  // In default mode (no --db), skip unconfigured providers\n  const isExplicitSelection = options.providers && options.providers.length > 0;\n  if (!isExplicitSelection) {\n    providers = providers.filter((name) => isProviderConfigured(name, config));\n  }\n\n  if (providers.length === 0) {\n    return [];\n  }\n\n  // Execute count for each provider concurrently\n  const results: CountResult[] = await Promise.all(\n    providers.map(async (providerName): Promise<CountResult> => {\n      try {\n        const provider = createProviderInstance(providerName, config);\n        if (provider === null) {\n          return { provider: providerName, count: 0, error: 'Provider configuration incomplete' };\n        }\n\n        // Translate query\n        let translatedQuery: TranslatedQuery;\n        if (options.directQuery && options.providers?.length === 1) {\n          translatedQuery = {\n            native: options.directQuery,\n            provider: providerName,\n          };\n        } else {\n          translatedQuery = translateQueryForProvider(ast!, providerName);\n        }\n\n        const count = await provider.count(translatedQuery);\n        return { provider: providerName, count };\n      } catch (error) {\n        const errorMessage = error instanceof Error\n          ? error.message\n          : isProviderError(error)\n            ? error.message\n            : String(error);\n        return { provider: providerName, count: 0, error: errorMessage };\n      }\n    })\n  );\n\n  return results;\n}\n\n\n/**\n * Execute preview mode: get counts and first few titles without creating a session.\n */\nexport async function executePreview(\n  options: SearchCommandOptions,\n  config: Config,\n  maxTitles = 5\n): Promise<PreviewResult[]> {\n  let ast: QueryAST | undefined;\n\n  // Handle direct query mode\n  if (options.directQuery && options.providers && options.providers.length === 1) {\n    ast = {\n      name: options.sessionName ?? 'direct-query',\n      blocks: [\n        {\n          field: 'all',\n          terms: { keywords: [options.directQuery] },\n          operator: 'AND',\n        },\n      ],\n      filters: {},\n      overrides: {},\n    };\n  } else if (options.queryFile) {\n    const queryContent = await readFile(options.queryFile, 'utf-8');\n    ast = parseQueryString(queryContent);\n  } else {\n    return [];\n  }\n\n  // Determine which providers to use\n  let providers = getEnabledProviders(config, options.providers);\n\n  // In default mode (no --db), skip unconfigured providers\n  const isExplicitSelection = options.providers && options.providers.length > 0;\n  if (!isExplicitSelection) {\n    providers = providers.filter((name) => isProviderConfigured(name, config));\n  }\n\n  if (providers.length === 0) {\n    return [];\n  }\n\n  // Execute preview for each provider concurrently\n  const results: PreviewResult[] = await Promise.all(\n    providers.map(async (providerName): Promise<PreviewResult> => {\n      try {\n        const provider = createProviderInstance(providerName, config);\n        if (provider === null) {\n          return { provider: providerName, count: 0, titles: [], error: 'Provider configuration incomplete' };\n        }\n\n        // Translate query\n        let translatedQuery: TranslatedQuery;\n        if (options.directQuery && options.providers?.length === 1) {\n          translatedQuery = {\n            native: options.directQuery,\n            provider: providerName,\n          };\n        } else {\n          translatedQuery = translateQueryForProvider(ast!, providerName);\n        }\n\n        // Get count first\n        const count = await provider.count(translatedQuery);\n\n        // Collect first few articles for titles\n        const titles: string[] = [];\n        const searchOptions = { maxResults: maxTitles };\n\n        for await (const article of provider.search(translatedQuery, searchOptions)) {\n          titles.push(article.title);\n          if (titles.length >= maxTitles) {\n            break;\n          }\n        }\n\n        return { provider: providerName, count, titles };\n      } catch (error) {\n        const errorMessage = error instanceof Error\n          ? error.message\n          : isProviderError(error)\n            ? error.message\n            : String(error);\n        return { provider: providerName, count: 0, titles: [], error: errorMessage };\n      }\n    })\n  );\n\n  return results;\n}\n\n/**\n * Load all articles from a session's results files (YAML preferred, JSONL fallback).\n */\nasync function loadArticlesFromSession(\n  sessionsDir: string,\n  sessionId: string,\n  providers: ProviderName[]\n): Promise<Article[]> {\n  const articles: Article[] = [];\n  const sessionDir = join(sessionsDir, sessionId);\n\n  for (const provider of providers) {\n    const providerArticles = await loadResults(sessionDir, provider);\n    articles.push(...providerArticles);\n  }\n\n  return 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'search-hub@example.com',\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      };\n      if (providerConfig.api_key) {\n        pubmedOpts.apiKey = providerConfig.api_key;\n      }\n      return new PubMedProvider(pubmedOpts);\n    }\n    case 'eric':\n      return new ERICProvider({\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      });\n    case 'arxiv':\n      return new ArxivProvider({\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      });\n    case 'scopus': {\n      if (!providerConfig.api_key) {\n        console.warn(\n          `Warning: Scopus requires an API key. Set providers.scopus.api_key in config.\\n` +\n          `  → Get an API key at https://dev.elsevier.com/\\n` +\n          `  → Run: search-hub config providers.scopus.api_key \"your-key\"`\n        );\n        return null;\n      }\n      const scopusOpts: ScopusConfig = {\n        apiKey: providerConfig.api_key,\n        rateLimit: providerConfig.rate_limit,\n        timeout: providerConfig.timeout,\n        retries: providerConfig.retries,\n      };\n      if (providerConfig.inst_token) {\n        scopusOpts.instToken = providerConfig.inst_token;\n      }\n      return new ScopusProvider(scopusOpts);\n    }\n    default:\n      throw new Error(`Provider '${name}' is not implemented`);\n  }\n}\n\n/**\n * Translate a query AST for a specific provider.\n * Resolves provider-specific blocks/filters before translation.\n */\nfunction translateQueryForProvider(\n  ast: QueryAST,\n  provider: ProviderName\n): TranslatedQuery {\n  const resolved = resolveForProvider(ast, provider);\n  switch (provider) {\n    case 'pubmed':\n      return translatePubmed(resolved);\n    case 'eric':\n      return translateEric(resolved);\n    case 'arxiv':\n      return translateArxiv(resolved);\n    case 'scopus':\n      return translateScopus(resolved);\n    default:\n      throw new Error(`No translator for provider '${provider}'`);\n  }\n}\n\n/**\n * Get enabled providers from config, optionally filtered by user selection.\n */\nfunction getEnabledProviders(\n  config: Config,\n  requestedProviders?: ProviderName[]\n): ProviderName[] {\n  const enabledInConfig = IMPLEMENTED_PROVIDERS.filter(\n    (name) => config.providers[name].enabled\n  );\n\n  if (requestedProviders && requestedProviders.length > 0) {\n    return requestedProviders.filter((p) => enabledInConfig.includes(p));\n  }\n\n  return enabledInConfig;\n}\n\n/**\n * Execute a search across multiple providers.\n */\nexport async function executeSearch(\n  options: SearchCommandOptions,\n  sessionsDir: string,\n  config: Config,\n  showProgress = true\n): Promise<SearchExecutionResult> {\n  let ast: QueryAST | undefined;\n  let queryContent: string;\n  let queryFile: string;\n\n  // Handle direct query mode\n  if (options.directQuery && options.providers && options.providers.length === 1) {\n    queryFile = 'direct-query';\n\n    // For direct query, we create a minimal AST structure\n    ast = {\n      name: options.sessionName ?? 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See warning above for details.`;\n        results[providerName] = { hits: 0, retrieved: 0, error: configError };\n        await updateDatabaseStatus(\n          sessionId,\n          providerName,\n          {\n            status: 'failed',\n            completedAt: new Date().toISOString(),\n            error: {\n              code: 'CONFIG_ERROR',\n              message: configError,\n              retryable: false,\n            },\n          },\n          sessionsDir\n        );\n        continue;\n      }\n\n      // Translate query\n      let translatedQuery: TranslatedQuery;\n      if (options.directQuery && options.providers?.length === 1) {\n        // For direct query, use the native query string directly\n        translatedQuery = {\n          native: options.directQuery,\n          provider: providerName,\n        };\n      } else {\n        translatedQuery = translateQueryForProvider(ast, providerName);\n      }\n\n      // Write translated query to session\n      const queryPath = join(sessionsDir, sessionId, `${providerName}_query.txt`);\n      await writeFile(queryPath, translatedQuery.native, 'utf-8');\n\n      // Update database status to in_progress\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'in_progress',\n          startedAt: new Date().toISOString(),\n        },\n        sessionsDir\n      );\n\n      // Prepare results file path\n      const resultsPath = join(sessionsDir, sessionId, `${providerName}_results.jsonl`);\n\n      // Execute search\n      let retrievedCount = 0;\n      let totalHits = 0;\n\n      progress?.update(providerName, 0, 0, 'in_progress');\n\n      const searchOptions = {\n        maxResults: options.maxResults ?? config.providers[providerName].max_results,\n      };\n\n      for await (const article of provider.search(translatedQuery, searchOptions)) {\n        retrievedCount++;\n\n        // Write article to JSONL file\n        await appendFile(resultsPath, JSON.stringify(article) + '\\n', 'utf-8');\n\n        // Update progress (estimate total from first batch)\n        if (totalHits === 0) {\n          // Estimate total - this is provider-dependent, we'll use retrieved count as minimum\n          totalHits = Math.max(retrievedCount * 10, 100);\n        }\n        progress?.update(providerName, retrievedCount, totalHits, 'in_progress');\n      }\n\n      // Update final totals\n      totalHits = retrievedCount; // Use actual count as final total\n\n      // Mark as completed\n      progress?.complete(providerName);\n\n      // Convert JSONL to YAML for human-readable view\n      const yamlFilename = `${providerName}_results.yaml`;\n      const yamlPath = join(sessionsDir, sessionId, yamlFilename);\n      await convertResultsToYaml(resultsPath, yamlPath, {\n        provider: providerName,\n        queryName: ast.name,\n      });\n\n      // Update database status\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'completed',\n          completedAt: new Date().toISOString(),\n          totalHits,\n          retrievedCount,\n          files: {\n            query: `${providerName}_query.txt`,\n            results: `${providerName}_results.jsonl`,\n            resultsYaml: yamlFilename,\n          },\n        },\n        sessionsDir\n      );\n\n      // Collect warnings if provider supports them\n      const providerWarnings = 'getWarnings' in provider && typeof (provider as any).getWarnings === 'function'\n        ? 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package/dist/cli/e2e-helpers.d.ts

@@ -115,12 +115,14 @@ export declare const queryFixtures: {
         name: string;
         description: string;
         blocks: ({
+            id: string;
             field: "title_abstract";
             terms: {
                 keywords: string[];
             };
             operator: "AND";
         } | {
+            id: string;
             field: "keyword";
             terms: {
                 keywords: string[];
@@ -132,12 +134,13 @@ export declare const queryFixtures: {
             yearTo: number;
             languages: string[];
         };
-        overrides: {};
+        providers: {};
     };
     /** Query with MeSH terms (PubMed-specific) */
     withMesh: {
         name: string;
         blocks: {
+            id: string;
             field: "title_abstract";
             terms: {
                 keywords: string[];
@@ -146,7 +149,7 @@ export declare const queryFixtures: {
             operator: "AND";
         }[];
         filters: {};
-        overrides: {};
+        providers: {};
     };
 };
 /**

package/dist/cli/e2e-helpers.d.ts.map

@@ -1 +1 @@
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package/dist/cli/index.d.ts.map

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package/dist/cli/index.js

@@ -16,6 +16,7 @@ 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 { inspectQueryCommand, formatInspectOutput } from "./commands/query/inspect.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";
@@ -25,6 +26,7 @@ import { formatVerboseProviderDetails } from "./commands/search-utils.js";
 import { parseExportOptions, validateExportInput, deduplicateArticles, filterArticles, formatIds, formatJson, formatCslJson, formatJsonl } from "./commands/export.js";
 import { computeSummary, formatSummaryJson, formatSummary } from "./commands/summary.js";
 import { parseResultsOptions, validateResultsInput, formatResultsJson, formatResultsList } from "./commands/results.js";
+import { filterByQuery } from "./commands/query-filter.js";
 import { loadNotes, formatAllSessionNotes, formatNotesList, addNote, addAssessment } from "./commands/notes.js";
 import { computeDiff, computeQueryDiff, formatDiffJson, formatDiff } from "./commands/diff.js";
 import { validateMergeSources, mergeArticles, formatMergeJson, formatMergeOutput, createMergedSession } from "./commands/merge.js";
@@ -51,6 +53,7 @@ import { fileURLToPath } from "node:url";
 import { getSessionsDir } from "./utils/sessions-dir.js";
 import { expandPath } from "../utils/path.js";
 import { loadSessionArticles, loadSessionQuery } from "./commands/session-utils.js";
+import { parseIdentifierFile, checkCoverage, formatCheckResultJson, formatCheckResult } from "./commands/check.js";
 config({ quiet: true });
 function createProgram() {
   const program = new Command();
@@ -60,11 +63,11 @@ function createProgram() {
 Workflow:
   1. query init → edit → validate / --dry-run        Query preparation
   2. search --preview → search                       Preview & execute
-  3. results / summary / diff                        Inspect & compare
+  3. results / summary / diff / check                Inspect & verify
   4. review init → extract → merge → status          Systematic review
   5. register / export                               Output
 
-  Iterate: search v1 → search v2 → diff             Query refinement
+  Iterate: search → results -q → check → diff       Query refinement
 
 Quick Start:
   $ search-hub query init -o search.yaml        # Create query template
@@ -288,6 +291,36 @@ Examples:
       process.exitCode = EXIT_CODES.QUERY_ERROR;
     }
   });
+  queryCommand.command("inspect").description("Show how a query resolves per provider (block replacements and added filters)").argument("<file>", "path to query YAML file").option("--db <provider>", "show resolution for specific provider only").addHelpText("after", `
+Examples:
+  $ search-hub query inspect ./diabetes-ai.yaml            # All databases
+  $ search-hub query inspect ./diabetes-ai.yaml --db pubmed # PubMed only`).action(async (file, options) => {
+    const globalOpts = program.opts();
+    try {
+      const inspectOptions = options.db ? { providers: [options.db] } : {};
+      const result = await inspectQueryCommand(file, inspectOptions);
+      if (!result.success) {
+        if (!globalOpts.quiet) {
+          console.error(`✗ Failed to inspect: ${file}
+  Error: ${result.error}`);
+        }
+        process.exitCode = EXIT_CODES.QUERY_ERROR;
+        return;
+      }
+      if (!globalOpts.quiet) {
+        console.log(formatInspectOutput(result.result));
+      }
+      process.exitCode = EXIT_CODES.SUCCESS;
+    } catch (error) {
+      if (!globalOpts.quiet) {
+        console.error(
+          "Error:",
+          error instanceof Error ? error.message : error
+        );
+      }
+      process.exitCode = EXIT_CODES.QUERY_ERROR;
+    }
+  });
   queryCommand.command("init").description("Generate a template query YAML file").option("-o, --output <path>", "write to file (default: stdout)").option("--force", "overwrite existing file", false).action(async (options) => {
     const globalOpts = program.opts();
     try {
@@ -376,7 +409,7 @@ Query features (use "query init" to see full template):
   filters:    year_from, year_to, language, publication_types
   exclude:    NOT terms per block (terms.exclude)
   mesh/eric:  controlled vocabulary (terms.mesh, terms.eric)
-  overrides:  per-database settings (pubmed, scopus, eric, arxiv)`).action(
+  providers:  per-database block replacements and filter additions`).action(
     async (queryFile, options) => {
       const globalOpts = program.opts();
       try {
@@ -695,25 +728,44 @@ Resume completed. ${execResult.resumed} provider(s) resumed.`);
       }
     }
   );
-  program.command("export").description("Export session results to various formats").argument("<session-id>", "session ID to export").option("--format <fmt>", "output format: ids, json, jsonl, csl-json", "jsonl").option("-o, --output <path>", "output file path (default: stdout)").option("--db <providers>", "export only specific database(s)").option("--id-type <type>", "for ids format: doi, pmid, all").option("--no-dedup", "disable deduplication of results").option("--filter-year <range>", 'year range filter (e.g., "2023-2025")').option("--filter-title <keywords>", "title keyword filter (comma-separated)").option("--filter-abstract <keywords>", "abstract keyword filter (comma-separated)").addHelpText("after", `
+  program.command("export").description("Export session results to various formats").argument("<session-id>", "session ID to export").option("--format <fmt>", "output format: ids, json, jsonl, csl-json", "jsonl").option("-o, --output <path>", "output file path (default: stdout)").option("--id-type <type>", "for ids format: doi, pmid, all").option("--no-dedup", "disable deduplication of results").option("-q, --query <expr>", "filter results with query expression").option("--filter-year <range>", "year range filter (deprecated, use -q)").option("--filter-title <keywords>", "title keyword filter (deprecated, use -q)").option("--filter-abstract <keywords>", "abstract keyword filter (deprecated, use -q)").addHelpText("after", `
 Examples:
   $ search-hub export SESSION_ID                             # JSONL to stdout
   $ search-hub export SESSION_ID --format json               # JSON to stdout
+  $ search-hub export SESSION_ID -q "year:2023"              # Filter by query
+  $ search-hub export SESSION_ID -q "author:smith" --format ids  # Filtered IDs
   $ search-hub export SESSION_ID --format json -o results.json  # JSON to file
   $ search-hub export SESSION_ID --format ids --id-type doi  # Export DOIs to stdout
-  $ search-hub export SESSION_ID --format csl-json -o refs.json  # CSL-JSON to file
-  $ search-hub export SESSION_ID --db pubmed --format jsonl
   $ search-hub export SESSION_ID --no-dedup  # Export without deduplication
   $ search-hub export SESSION_ID --format jsonl | jq '.title'  # Pipe to jq
-  $ search-hub export SESSION_ID --filter-year 2023-2025     # Filter by year
-  $ search-hub export SESSION_ID --filter-title "machine learning,AI"  # Filter by title`).action(
+
+Query syntax:
+  Free text        diabetes             Search title and abstract
+  title:VALUE      title:learning       Title substring
+  abstract:VALUE   abstract:randomized  Abstract substring
+  author:VALUE     author:tanaka        Author name substring
+  journal:VALUE    journal:lancet       Journal name substring
+  year:VALUE       year:2023            Exact year
+  year:FROM-TO     year:2020-2024       Year range
+  doi:VALUE        doi:10.1001/xxx      DOI exact match
+  pmid:VALUE       pmid:12345678        PMID exact match
+  source:VALUE     source:pubmed        Provider exact match
+
+  Multiple terms: different fields = AND, same field = OR`).action(
     async (sessionId, options) => {
       const globalOpts = program.opts();
       try {
+        const hasLegacyFilter = options?.filterYear || options?.filterTitle || options?.filterAbstract;
+        if (options?.query && hasLegacyFilter) {
+          if (!globalOpts.quiet) {
+            console.error("Error: Cannot use -q/--query together with --filter-year, --filter-title, or --filter-abstract. Use -q only.");
+          }
+          process.exitCode = EXIT_CODES.SESSION_ERROR;
+          return;
+        }
         const exportOpts = parseExportOptions(sessionId, {
           format: options?.format,
           output: options?.output,
-          db: options?.db,
           idType: options?.idType
         });
         const validation = validateExportInput(exportOpts);
@@ -737,7 +789,7 @@ Examples:
           process.exitCode = EXIT_CODES.SESSION_ERROR;
           return;
         }
-        const articles = await loadSessionArticles(session, sessionId, sessionsDir, exportOpts.providers);
+        const articles = await loadSessionArticles(session, sessionId, sessionsDir);
         const shouldDedup = options?.dedup !== false;
         let exportArticles;
         let duplicatesRemoved = 0;
@@ -748,32 +800,38 @@ Examples:
         } else {
           exportArticles = articles;
         }
-        const filter = {};
-        if (options?.filterYear) {
-          const parts = options.filterYear.split("-");
-          if (parts.length === 2) {
-            const from = parseInt(parts[0], 10);
-            const to = parseInt(parts[1], 10);
-            if (!Number.isNaN(from)) filter.yearFrom = from;
-            if (!Number.isNaN(to)) filter.yearTo = to;
-          } else if (parts.length === 1) {
-            const year = parseInt(parts[0], 10);
-            if (!Number.isNaN(year)) {
-              filter.yearFrom = year;
-              filter.yearTo = year;
+        const preFilterCount = exportArticles.length;
+        let hasFilter = false;
+        if (options?.query) {
+          exportArticles = filterByQuery(exportArticles, options.query);
+          hasFilter = true;
+        } else {
+          const filter = {};
+          if (options?.filterYear) {
+            const parts = options.filterYear.split("-");
+            if (parts.length === 2) {
+              const from = parseInt(parts[0], 10);
+              const to = parseInt(parts[1], 10);
+              if (!Number.isNaN(from)) filter.yearFrom = from;
+              if (!Number.isNaN(to)) filter.yearTo = to;
+            } else if (parts.length === 1) {
+              const year = parseInt(parts[0], 10);
+              if (!Number.isNaN(year)) {
+                filter.yearFrom = year;
+                filter.yearTo = year;
+              }
             }
           }
-        }
-        if (options?.filterTitle) {
-          filter.titleKeywords = options.filterTitle.split(",").map((s) => s.trim()).filter(Boolean);
-        }
-        if (options?.filterAbstract) {
-          filter.abstractKeywords = options.filterAbstract.split(",").map((s) => s.trim()).filter(Boolean);
-        }
-        const preFilterCount = exportArticles.length;
-        const hasFilter = filter.yearFrom !== void 0 || filter.yearTo !== void 0 || filter.titleKeywords && filter.titleKeywords.length > 0 || filter.abstractKeywords && filter.abstractKeywords.length > 0;
-        if (hasFilter) {
-          exportArticles = filterArticles(exportArticles, filter);
+          if (options?.filterTitle) {
+            filter.titleKeywords = options.filterTitle.split(",").map((s) => s.trim()).filter(Boolean);
+          }
+          if (options?.filterAbstract) {
+            filter.abstractKeywords = options.filterAbstract.split(",").map((s) => s.trim()).filter(Boolean);
+          }
+          hasFilter = !!(filter.yearFrom !== void 0 || filter.yearTo !== void 0 || filter.titleKeywords && filter.titleKeywords.length > 0 || filter.abstractKeywords && filter.abstractKeywords.length > 0);
+          if (hasFilter) {
+            exportArticles = filterArticles(exportArticles, filter);
+          }
         }
         let output;
         if (exportOpts.format === "ids") {
@@ -881,15 +939,30 @@ Examples:
       }
     }
   );
-  program.command("results").description("List articles from a session with title, year, and journal").argument("<session-id>", "session ID to list results from").option("--limit <n>", "maximum number of results to show").option("--offset <n>", "skip first n results").option("--json", "output as JSON array").option("--fields <fields>", "fields to display (comma-separated)").option("--db <providers>", "filter by database(s), comma-separated").option("--filter-year <range>", 'year range filter (e.g., "2023-2025")').option("--filter-title <keywords>", "title keyword filter (comma-separated)").option("--filter-abstract <keywords>", "abstract keyword filter (comma-separated)").option("--abstract", "show abstracts with results").option("--abstract-length <n>", "maximum abstract length in characters (default: 300)").addHelpText("after", `
+  program.command("results").description("List articles from a session with title, year, and journal").argument("<session-id>", "session ID to list results from").option("--limit <n>", "maximum number of results to show").option("--offset <n>", "skip first n results").option("--json", "output as JSON array").option("--fields <fields>", "fields to display (comma-separated)").option("-q, --query <expr>", "filter results with query expression").option("--filter-year <range>", "year range filter (deprecated, use -q)").option("--filter-title <keywords>", "title keyword filter (deprecated, use -q)").option("--filter-abstract <keywords>", "abstract keyword filter (deprecated, use -q)").option("--abstract", "show abstracts with results").option("--abstract-length <n>", "maximum abstract length in characters (default: 300)").addHelpText("after", `
 Examples:
-  $ search-hub results SESSION_ID                         # List all articles
-  $ search-hub results SESSION_ID --limit 20              # First 20 articles
-  $ search-hub results SESSION_ID --limit 20 --offset 40  # Articles 41-60
-  $ search-hub results SESSION_ID --json                  # JSON output for scripting
-  $ search-hub results SESSION_ID --db pubmed             # Only PubMed articles
-  $ search-hub results SESSION_ID --filter-year 2023-2025 # Filter by year
-  $ search-hub results SESSION_ID --abstract              # Show with abstracts`).action(
+  $ search-hub results SESSION_ID                              # List all articles
+  $ search-hub results SESSION_ID --limit 20                   # First 20 articles
+  $ search-hub results SESSION_ID -q "diabetes"                # Free text filter
+  $ search-hub results SESSION_ID -q "author:smith year:2023"  # Combined filter
+  $ search-hub results SESSION_ID -q "doi:10.1001/xxx"         # Exact ID match
+  $ search-hub results SESSION_ID --json                       # JSON output
+  $ search-hub results SESSION_ID -q "source:pubmed"           # Only PubMed
+  $ search-hub results SESSION_ID --abstract                   # Show abstracts
+
+Query syntax:
+  Free text        diabetes             Search title and abstract
+  title:VALUE      title:learning       Title substring
+  abstract:VALUE   abstract:randomized  Abstract substring
+  author:VALUE     author:tanaka        Author name substring
+  journal:VALUE    journal:lancet       Journal name substring
+  year:VALUE       year:2023            Exact year
+  year:FROM-TO     year:2020-2024       Year range
+  doi:VALUE        doi:10.1001/xxx      DOI exact match
+  pmid:VALUE       pmid:12345678        PMID exact match
+  source:VALUE     source:pubmed        Provider exact match
+
+  Multiple terms: different fields = AND, same field = OR`).action(
     async (sessionId, options) => {
       const globalOpts = program.opts();
       try {
@@ -898,7 +971,7 @@ Examples:
           offset: options?.offset,
           json: options?.json,
           fields: options?.fields,
-          db: options?.db,
+          query: options?.query,
           filterYear: options?.filterYear,
           filterTitle: options?.filterTitle,
           filterAbstract: options?.filterAbstract,
@@ -926,11 +999,17 @@ Examples:
           process.exitCode = EXIT_CODES.SESSION_ERROR;
           return;
         }
-        const articles = await loadSessionArticles(session, sessionId, sessionsDir, resultsOpts.providers);
+        const articles = await loadSessionArticles(session, sessionId, sessionsDir);
         const dedupResult = deduplicateArticles(articles);
         let displayArticles = dedupResult.articles;
         let filteredFrom;
-        if (resultsOpts.filter) {
+        if (resultsOpts.query) {
+          const preFilterCount = displayArticles.length;
+          displayArticles = filterByQuery(displayArticles, resultsOpts.query);
+          if (displayArticles.length !== preFilterCount) {
+            filteredFrom = preFilterCount;
+          }
+        } else if (resultsOpts.filter) {
           const preFilterCount = displayArticles.length;
           displayArticles = filterArticles(displayArticles, resultsOpts.filter);
           if (displayArticles.length !== preFilterCount) {
@@ -1072,6 +1151,110 @@ Query Refinement Workflow:
       }
     }
   );
+  program.command("check").description("Verify coverage of known articles against session results").argument("<session-id>", "session ID to check against").option("--file <path>", "file with identifiers (one per line)").option("--doi <ids>", "comma-separated DOIs to check").option("--pmid <ids>", "comma-separated PMIDs to check").option("--json", "output as JSON").option("--missing-only", "show only missing identifiers").addHelpText("after", `
+Examples:
+  $ search-hub check SESSION --file known-dois.txt              # Check from file
+  $ search-hub check SESSION --doi "10.1001/jama.2023.12345"    # Check single DOI
+  $ search-hub check SESSION --pmid "37654321,36543210"         # Check PMIDs
+  $ search-hub check SESSION --file refs.txt --json             # JSON output
+  $ search-hub check SESSION --file refs.txt --missing-only     # Only missing
+
+Input file format (one identifier per line):
+  10.1001/jama.2023.12345          DOI (starts with "10.")
+  37654321                          PMID (numeric only)
+  DOI:10.1038/s41586-023-xxxxx    DOI (explicit prefix)
+  PMID:36543210                    PMID (explicit prefix)
+  arxiv:2301.12345                 arXiv ID (explicit prefix)
+  # comment                        Comments and empty lines ignored`).action(
+    async (sessionId, options) => {
+      const globalOpts = program.opts();
+      try {
+        let identifiers;
+        let source;
+        if (options?.file) {
+          const filePath = expandPath(options.file);
+          let content;
+          try {
+            content = await readFile(filePath, "utf-8");
+          } catch {
+            if (!globalOpts.quiet) {
+              console.error(`Error: File not found: ${filePath}`);
+            }
+            process.exitCode = EXIT_CODES.GENERAL_ERROR;
+            return;
+          }
+          try {
+            identifiers = parseIdentifierFile(content);
+          } catch (error) {
+            if (!globalOpts.quiet) {
+              console.error(`Error: ${error instanceof Error ? error.message : "Failed to parse identifier file"}`);
+            }
+            process.exitCode = EXIT_CODES.GENERAL_ERROR;
+            return;
+          }
+          source = options.file;
+        } else if (options?.doi || options?.pmid) {
+          const lines = [];
+          if (options.doi) {
+            lines.push(...options.doi.split(",").map((d) => d.trim()).filter(Boolean));
+          }
+          if (options.pmid) {
+            lines.push(...options.pmid.split(",").map((p) => `PMID:${p.trim()}`).filter(Boolean));
+          }
+          identifiers = parseIdentifierFile(lines.join("\n"));
+          source = "command line";
+        } else {
+          if (!globalOpts.quiet) {
+            console.error("Error: Provide --file, --doi, or --pmid");
+          }
+          process.exitCode = EXIT_CODES.GENERAL_ERROR;
+          return;
+        }
+        if (identifiers.length === 0) {
+          if (!globalOpts.quiet) {
+            console.error("Error: No identifiers found in input");
+          }
+          process.exitCode = EXIT_CODES.GENERAL_ERROR;
+          return;
+        }
+        const sessionsDir = await getSessionsDir(globalOpts);
+        let session;
+        try {
+          session = await loadSession(sessionId, sessionsDir);
+        } catch (error) {
+          if (!globalOpts.quiet) {
+            console.error(
+              `Error: ${error instanceof Error ? error.message : "Failed to load session"}`
+            );
+          }
+          process.exitCode = EXIT_CODES.SESSION_ERROR;
+          return;
+        }
+        const articles = await loadSessionArticles(session, sessionId, sessionsDir);
+        const result = checkCoverage(articles, identifiers);
+        if (options?.json) {
+          console.log(formatCheckResultJson(result, { sessionId, source }));
+        } else {
+          if (!globalOpts.quiet) {
+            console.log(formatCheckResult(result, {
+              sessionId,
+              source,
+              missingOnly: options?.missingOnly
+            }));
+          }
+        }
+        process.exitCode = EXIT_CODES.SUCCESS;
+      } catch (error) {
+        if (!globalOpts.quiet) {
+          console.error(
+            "Error:",
+            error instanceof Error ? error.message : error
+          );
+        }
+        process.exitCode = EXIT_CODES.GENERAL_ERROR;
+      }
+    }
+  );
   program.command("merge").description("Merge results from multiple search sessions").argument("<session-ids...>", "two or more session IDs to merge").option("--name <string>", "name for merged session").option("--dry-run", "show what would be merged without creating session").option("--json", "output as JSON").addHelpText("after", `
 Examples:
   $ search-hub merge session-v4 session-v9                  # Merge two sessions