@ncukondo/search-hub 0.1.0

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

@@ -0,0 +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 } 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 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 type { RegistrationRecord } from '../../integration/types.js';\nimport { checkRefAvailable } from '../../integration/ref-cli.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 }>;\n  error?: string;\n  autoRegisterResult?: RegistrationRecord;\n}\n\n/**\n * Available providers that are implemented.\n */\nconst IMPLEMENTED_PROVIDERS: ProviderName[] = ['pubmed', 'eric', 'arxiv', 'scopus'];\n\n/**\n * Create a provider instance for the given provider name.\n */\nexport function createProviderInstance(\n  name: ProviderName,\n  config: Config\n): Provider {\n  const providerConfig = config.providers[name];\n\n  switch (name) {\n    case 'pubmed': {\n      if (!providerConfig.email) {\n        console.warn(\n          'Warning: No email configured for PubMed. Set providers.pubmed.email in config.'\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      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        error: `Failed to parse query file: ${error instanceof Error ? error.message : error}`,\n      };\n    }\n  } else {\n    return {\n      success: false,\n      error: 'Either queryFile or directQuery with provider is required',\n    };\n  }\n\n  // Determine which providers to use\n  const providers = getEnabledProviders(config, options.providers);\n\n  if (providers.length === 0) {\n    return {\n      success: false,\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      error: `Failed to create session: ${error instanceof Error ? error.message : error}`,\n    };\n  }\n\n  const sessionId = session.id;\n  const results: Record<string, { hits: number; retrieved: number }> = {};\n\n  // Create progress display if enabled\n  let progress: MultiProviderProgress | undefined;\n  if (showProgress && process.stdout.isTTY) {\n    progress = new MultiProviderProgress(providers);\n  }\n\n  // Execute search for each provider\n  for (const providerName of providers) {\n    try {\n      // Create provider instance\n      const provider = createProviderInstance(providerName, config);\n\n      // Translate query\n      let translatedQuery: TranslatedQuery;\n      if (options.directQuery && options.providers?.length === 1) {\n        // For direct query, use the native query string directly\n        translatedQuery = {\n          native: options.directQuery,\n          provider: providerName,\n        };\n      } else {\n        translatedQuery = translateQueryForProvider(ast, providerName);\n      }\n\n      // Write translated query to session\n      const queryPath = join(sessionsDir, sessionId, `${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, `${providerName}_results.jsonl`);\n\n      // Execute search\n      let retrievedCount = 0;\n      let totalHits = 0;\n\n      progress?.update(providerName, 0, 0, 'in_progress');\n\n      const searchOptions = {\n        maxResults: options.maxResults ?? config.providers[providerName].max_results,\n      };\n\n      for await (const article of provider.search(translatedQuery, searchOptions)) {\n        retrievedCount++;\n\n        // Write article to JSONL file\n        await appendFile(resultsPath, JSON.stringify(article) + '\\n', 'utf-8');\n\n        // Update progress (estimate total from first batch)\n        if (totalHits === 0) {\n          // Estimate total - this is provider-dependent, we'll use retrieved count as minimum\n          totalHits = Math.max(retrievedCount * 10, 100);\n        }\n        progress?.update(providerName, retrievedCount, totalHits, 'in_progress');\n      }\n\n      // Update final totals\n      totalHits = retrievedCount; // Use actual count as final total\n\n      // Mark as completed\n      progress?.complete(providerName);\n\n      // Update database status\n      await updateDatabaseStatus(\n        sessionId,\n        providerName,\n        {\n          status: 'completed',\n          completedAt: new Date().toISOString(),\n          totalHits,\n          retrievedCount,\n          files: {\n            query: `${providerName}_query.txt`,\n            results: `${providerName}_results.jsonl`,\n          },\n        },\n        sessionsDir\n      );\n\n      results[providerName] = { hits: totalHits, retrieved: retrievedCount };\n    } catch (error) {\n      const errorMessage = error instanceof Error ? error.message : 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 };\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.retrieved === 0 && r.hits === 0;\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      results,\n      error: 'All providers failed',\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  };\n\n  if (autoRegisterResult) {\n    result.autoRegisterResult = autoRegisterResult;\n  }\n\n  return result;\n}\n\n/**\n * Load all articles from a session's results files.\n */\nasync function loadArticlesFromSession(\n  sessionsDir: string,\n  sessionId: string,\n  providers: ProviderName[]\n): Promise<Article[]> {\n  const articles: Article[] = [];\n\n  for (const provider of providers) {\n    const resultsPath = join(sessionsDir, sessionId, `${provider}_results.jsonl`);\n    try {\n      const content = await readFile(resultsPath, 'utf-8');\n      const lines = content.trim().split('\\n').filter((line) => line.length > 0);\n      for (const line of lines) {\n        try {\n          const article = JSON.parse(line) as Article;\n          articles.push(article);\n        } catch {\n          // Skip invalid JSON lines\n        }\n      }\n    } catch {\n      // Skip if file doesn't exist\n    }\n  }\n\n  return 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package/dist/cli/commands/search.d.ts

@@ -0,0 +1,30 @@
+import { ProviderName } from '../../session/types.js';
+export interface SearchCommandOptions {
+    queryFile?: string;
+    directQuery?: string;
+    providers?: ProviderName[];
+    sessionName?: string;
+    maxResults?: number;
+    dryRun?: boolean;
+    noResume?: boolean;
+}
+export interface CommandLineOptions {
+    db?: string | undefined;
+    query?: string | undefined;
+    name?: string | undefined;
+    maxResults?: string | undefined;
+    dryRun?: boolean | undefined;
+    noResume?: boolean | undefined;
+}
+export interface TranslationResult {
+    provider: string;
+    query: string;
+}
+export interface ValidationResult {
+    valid: boolean;
+    error?: string;
+}
+export declare function parseSearchOptions(queryFile: string | undefined, options: CommandLineOptions): SearchCommandOptions;
+export declare function validateSearchInput(options: SearchCommandOptions): ValidationResult;
+export declare function formatDryRunOutput(translations: TranslationResult[]): string;
+//# sourceMappingURL=search.d.ts.map

package/dist/cli/commands/search.d.ts.map

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package/dist/cli/commands/search.js

@@ -0,0 +1,67 @@
+import { parseProviderNames } from "../utils/validation.js";
+function parseSearchOptions(queryFile, options) {
+  const result = {};
+  if (queryFile) {
+    result.queryFile = queryFile;
+  }
+  if (options.query) {
+    result.directQuery = options.query;
+  }
+  if (options.db) {
+    result.providers = parseProviderNames(options.db);
+  }
+  if (options.name) {
+    result.sessionName = options.name;
+  }
+  if (options.maxResults) {
+    result.maxResults = parseInt(options.maxResults, 10);
+  }
+  if (options.dryRun) {
+    result.dryRun = true;
+  }
+  if (options.noResume) {
+    result.noResume = true;
+  }
+  return result;
+}
+function validateSearchInput(options) {
+  if (!options.queryFile && !options.directQuery) {
+    return {
+      valid: false,
+      error: "Either a query file or --query option is required"
+    };
+  }
+  if (options.directQuery && (!options.providers || options.providers.length === 0)) {
+    return {
+      valid: false,
+      error: "Direct query (--query) requires --db option to specify the provider"
+    };
+  }
+  if (options.directQuery && options.providers && options.providers.length > 1) {
+    return {
+      valid: false,
+      error: "Direct query (--query) can only be used with a single provider (--db)"
+    };
+  }
+  return { valid: true };
+}
+function formatDryRunOutput(translations) {
+  if (translations.length === 0) {
+    return "No translations available.";
+  }
+  const lines = [];
+  lines.push("Translated queries:");
+  lines.push("");
+  for (const t of translations) {
+    lines.push(`[${t.provider}]`);
+    lines.push(t.query);
+    lines.push("");
+  }
+  return lines.join("\n");
+}
+export {
+  formatDryRunOutput,
+  parseSearchOptions,
+  validateSearchInput
+};
+//# sourceMappingURL=search.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"search.js","sources":["../../../src/cli/commands/search.ts"],"sourcesContent":["import type { ProviderName } from '../../session/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\n\nexport interface SearchCommandOptions {\n  queryFile?: string;\n  directQuery?: string;\n  providers?: ProviderName[];\n  sessionName?: string;\n  maxResults?: number;\n  dryRun?: boolean;\n  noResume?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  query?: string | undefined;\n  name?: string | undefined;\n  maxResults?: string | undefined;\n  dryRun?: boolean | undefined;\n  noResume?: boolean | undefined;\n}\n\nexport interface TranslationResult {\n  provider: string;\n  query: string;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nexport function parseSearchOptions(\n  queryFile: string | undefined,\n  options: CommandLineOptions\n): SearchCommandOptions {\n  const result: SearchCommandOptions = {};\n\n  if (queryFile) {\n    result.queryFile = queryFile;\n  }\n\n  if (options.query) {\n    result.directQuery = options.query;\n  }\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.name) {\n    result.sessionName = options.name;\n  }\n\n  if (options.maxResults) {\n    result.maxResults = parseInt(options.maxResults, 10);\n  }\n\n  if (options.dryRun) {\n    result.dryRun = true;\n  }\n\n  if (options.noResume) {\n    result.noResume = true;\n  }\n\n  return result;\n}\n\nexport function validateSearchInput(options: SearchCommandOptions): ValidationResult {\n  // Case 1: Neither query file nor direct query\n  if (!options.queryFile && !options.directQuery) {\n    return {\n      valid: false,\n      error: 'Either a query file or --query option is required',\n    };\n  }\n\n  // Case 2: Direct query without provider\n  if (options.directQuery && (!options.providers || options.providers.length === 0)) {\n    return {\n      valid: false,\n      error: 'Direct query (--query) requires --db option to specify the provider',\n    };\n  }\n\n  // Case 3: Direct query with multiple providers\n  if (options.directQuery && options.providers && options.providers.length > 1) {\n    return {\n      valid: false,\n      error: 'Direct query (--query) can only be used with a single provider (--db)',\n    };\n  }\n\n  return { valid: true };\n}\n\nexport function formatDryRunOutput(translations: TranslationResult[]): string {\n  if (translations.length === 0) {\n    return 'No translations available.';\n  }\n\n  const lines: string[] = [];\n  lines.push('Translated queries:');\n  lines.push('');\n\n  for (const t of translations) {\n    lines.push(`[${t.provider}]`);\n    lines.push(t.query);\n    lines.push('');\n  }\n\n  return lines.join('\\n');\n}\n"],"names":[],"mappings":";AAgCO,SAAS,mBACd,WACA,SACsB;AACtB,QAAM,SAA+B,CAAA;AAErC,MAAI,WAAW;AACb,WAAO,YAAY;AAAA,EACrB;AAEA,MAAI,QAAQ,OAAO;AACjB,WAAO,cAAc,QAAQ;AAAA,EAC/B;AAEA,MAAI,QAAQ,IAAI;AACd,WAAO,YAAY,mBAAmB,QAAQ,EAAE;AAAA,EAClD;AAEA,MAAI,QAAQ,MAAM;AAChB,WAAO,cAAc,QAAQ;AAAA,EAC/B;AAEA,MAAI,QAAQ,YAAY;AACtB,WAAO,aAAa,SAAS,QAAQ,YAAY,EAAE;AAAA,EACrD;AAEA,MAAI,QAAQ,QAAQ;AAClB,WAAO,SAAS;AAAA,EAClB;AAEA,MAAI,QAAQ,UAAU;AACpB,WAAO,WAAW;AAAA,EACpB;AAEA,SAAO;AACT;AAEO,SAAS,oBAAoB,SAAiD;AAEnF,MAAI,CAAC,QAAQ,aAAa,CAAC,QAAQ,aAAa;AAC9C,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,MAAI,QAAQ,gBAAgB,CAAC,QAAQ,aAAa,QAAQ,UAAU,WAAW,IAAI;AACjF,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAGA,MAAI,QAAQ,eAAe,QAAQ,aAAa,QAAQ,UAAU,SAAS,GAAG;AAC5E,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAEA,SAAO,EAAE,OAAO,KAAA;AAClB;AAEO,SAAS,mBAAmB,cAA2C;AAC5E,MAAI,aAAa,WAAW,GAAG;AAC7B,WAAO;AAAA,EACT;AAEA,QAAM,QAAkB,CAAA;AACxB,QAAM,KAAK,qBAAqB;AAChC,QAAM,KAAK,EAAE;AAEb,aAAW,KAAK,cAAc;AAC5B,UAAM,KAAK,IAAI,EAAE,QAAQ,GAAG;AAC5B,UAAM,KAAK,EAAE,KAAK;AAClB,UAAM,KAAK,EAAE;AAAA,EACf;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

package/dist/cli/commands/status.d.ts

@@ -0,0 +1,41 @@
+export interface SessionListItem {
+    id: string;
+    name: string;
+    status: string;
+    createdAt: string;
+    progress: string;
+}
+export interface DatabaseDetails {
+    provider: string;
+    status: string;
+    totalHits: number;
+    retrievedCount: number;
+    error?: string;
+}
+export interface SessionDetails {
+    id: string;
+    name: string;
+    description?: string;
+    status: string;
+    createdAt: string;
+    updatedAt: string;
+    queryFile: string;
+    totalHits: number;
+    totalRetrieved: number;
+    databases: DatabaseDetails[];
+}
+export interface ListOptions {
+    all: boolean;
+}
+export interface FormatOptions {
+    json: boolean;
+}
+export declare function listSessionsForDisplay(sessionsDir: string, options: ListOptions): Promise<SessionListItem[]>;
+export declare function getSessionDetails(sessionId: string, sessionsDir: string): Promise<{
+    success: boolean;
+    session?: SessionDetails;
+    error?: string;
+}>;
+export declare function formatSessionList(sessions: SessionListItem[], options: FormatOptions): string;
+export declare function formatSessionDetails(details: SessionDetails, options: FormatOptions): string;
+//# sourceMappingURL=status.d.ts.map

package/dist/cli/commands/status.d.ts.map

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package/dist/cli/commands/status.js

@@ -0,0 +1,123 @@
+import { loadSession, listSessions } from "../../session/manager.js";
+async function listSessionsForDisplay(sessionsDir, options) {
+  const summaries = await listSessions(sessionsDir);
+  const filtered = options.all ? summaries : summaries.filter((s) => s.status !== "completed");
+  return filtered.map((s) => ({
+    id: s.id,
+    name: s.name,
+    status: s.status,
+    createdAt: s.createdAt,
+    progress: `${s.totalRetrieved}/${s.totalHits}`
+  }));
+}
+async function getSessionDetails(sessionId, sessionsDir) {
+  try {
+    const session = await loadSession(sessionId, sessionsDir);
+    const databases = [];
+    for (const [provider, dbStatus] of Object.entries(session.databases)) {
+      if (!dbStatus) continue;
+      const dbDetail = {
+        provider,
+        status: dbStatus.status,
+        totalHits: dbStatus.totalHits ?? 0,
+        retrievedCount: dbStatus.retrievedCount ?? 0
+      };
+      if (dbStatus.error?.message) {
+        dbDetail.error = dbStatus.error.message;
+      }
+      databases.push(dbDetail);
+    }
+    const sessionDetails = {
+      id: session.id,
+      name: session.name,
+      status: session.summary.status,
+      createdAt: session.createdAt,
+      updatedAt: session.updatedAt,
+      queryFile: session.query.file,
+      totalHits: session.summary.totalHits,
+      totalRetrieved: session.summary.totalRetrieved,
+      databases
+    };
+    if (session.description) {
+      sessionDetails.description = session.description;
+    }
+    return {
+      success: true,
+      session: sessionDetails
+    };
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Unknown error";
+    return {
+      success: false,
+      error: message
+    };
+  }
+}
+function formatSessionList(sessions, options) {
+  if (options.json) {
+    return JSON.stringify(sessions, null, 2);
+  }
+  if (sessions.length === 0) {
+    return "No sessions found.";
+  }
+  const header = `${"ID".padEnd(35)} ${"NAME".padEnd(20)} ${"STATUS".padEnd(15)} ${"PROGRESS".padEnd(12)} CREATED`;
+  const separator = "-".repeat(100);
+  const rows = sessions.map((s) => {
+    const date = new Date(s.createdAt).toLocaleDateString();
+    return `${s.id.padEnd(35)} ${s.name.padEnd(20)} ${s.status.padEnd(15)} ${s.progress.padEnd(12)} ${date}`;
+  });
+  return [header, separator, ...rows].join("\n");
+}
+function formatSessionDetails(details, options) {
+  if (options.json) {
+    return JSON.stringify(details, null, 2);
+  }
+  const lines = [];
+  lines.push(`Session: ${details.name}`);
+  lines.push(`ID: ${details.id}`);
+  if (details.description) {
+    lines.push(`Description: ${details.description}`);
+  }
+  lines.push(`Status: ${details.status}`);
+  lines.push(`Query File: ${details.queryFile}`);
+  lines.push(`Created: ${new Date(details.createdAt).toLocaleString()}`);
+  lines.push(`Updated: ${new Date(details.updatedAt).toLocaleString()}`);
+  lines.push("");
+  lines.push(`Total: ${details.totalRetrieved}/${details.totalHits} results`);
+  lines.push("");
+  lines.push("Databases:");
+  for (const db of details.databases) {
+    const statusIcon = getStatusIcon(db.status);
+    let line = `  ${statusIcon} ${db.provider.padEnd(10)} ${db.status.padEnd(12)} ${db.retrievedCount}/${db.totalHits}`;
+    if (db.error) {
+      line += ` (${db.error})`;
+    }
+    lines.push(line);
+  }
+  return lines.join("\n");
+}
+function getStatusIcon(status) {
+  switch (status) {
+    case "completed":
+      return "✓";
+    // ✓
+    case "failed":
+      return "✗";
+    // ✗
+    case "in_progress":
+      return "⠋";
+    // ⠋
+    case "pending":
+      return "◼";
+    // ◼
+    default:
+      return " ";
+  }
+}
+export {
+  formatSessionDetails,
+  formatSessionList,
+  getSessionDetails,
+  listSessionsForDisplay
+};
+//# sourceMappingURL=status.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"status.js","sources":["../../../src/cli/commands/status.ts"],"sourcesContent":["import { listSessions, loadSession } from '../../session/manager.js';\n\nexport interface SessionListItem {\n  id: string;\n  name: string;\n  status: string;\n  createdAt: string;\n  progress: string;\n}\n\nexport interface DatabaseDetails {\n  provider: string;\n  status: string;\n  totalHits: number;\n  retrievedCount: number;\n  error?: string;\n}\n\nexport interface SessionDetails {\n  id: string;\n  name: string;\n  description?: string;\n  status: string;\n  createdAt: string;\n  updatedAt: string;\n  queryFile: string;\n  totalHits: number;\n  totalRetrieved: number;\n  databases: DatabaseDetails[];\n}\n\nexport interface ListOptions {\n  all: boolean;\n}\n\nexport interface FormatOptions {\n  json: boolean;\n}\n\nexport async function listSessionsForDisplay(\n  sessionsDir: string,\n  options: ListOptions\n): Promise<SessionListItem[]> {\n  const summaries = await listSessions(sessionsDir);\n\n  const filtered = options.all\n    ? summaries\n    : summaries.filter((s) => s.status !== 'completed');\n\n  return filtered.map((s) => ({\n    id: s.id,\n    name: s.name,\n    status: s.status,\n    createdAt: s.createdAt,\n    progress: `${s.totalRetrieved}/${s.totalHits}`,\n  }));\n}\n\nexport async function getSessionDetails(\n  sessionId: string,\n  sessionsDir: string\n): Promise<{ success: boolean; session?: SessionDetails; error?: string }> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    const databases: DatabaseDetails[] = [];\n    for (const [provider, dbStatus] of Object.entries(session.databases)) {\n      if (!dbStatus) continue;\n      const dbDetail: DatabaseDetails = {\n        provider,\n        status: dbStatus.status,\n        totalHits: dbStatus.totalHits ?? 0,\n        retrievedCount: dbStatus.retrievedCount ?? 0,\n      };\n      if (dbStatus.error?.message) {\n        dbDetail.error = dbStatus.error.message;\n      }\n      databases.push(dbDetail);\n    }\n\n    const sessionDetails: SessionDetails = {\n      id: session.id,\n      name: session.name,\n      status: session.summary.status,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      queryFile: session.query.file,\n      totalHits: session.summary.totalHits,\n      totalRetrieved: session.summary.totalRetrieved,\n      databases,\n    };\n    if (session.description) {\n      sessionDetails.description = session.description;\n    }\n\n    return {\n      success: true,\n      session: sessionDetails,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n\nexport function formatSessionList(\n  sessions: SessionListItem[],\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(sessions, null, 2);\n  }\n\n  if (sessions.length === 0) {\n    return 'No sessions found.';\n  }\n\n  const header = `${'ID'.padEnd(35)} ${'NAME'.padEnd(20)} ${'STATUS'.padEnd(15)} ${'PROGRESS'.padEnd(12)} CREATED`;\n  const separator = '-'.repeat(100);\n\n  const rows = sessions.map((s) => {\n    const date = new Date(s.createdAt).toLocaleDateString();\n    return `${s.id.padEnd(35)} ${s.name.padEnd(20)} ${s.status.padEnd(15)} ${s.progress.padEnd(12)} ${date}`;\n  });\n\n  return [header, separator, ...rows].join('\\n');\n}\n\nexport function formatSessionDetails(\n  details: SessionDetails,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(details, null, 2);\n  }\n\n  const lines: string[] = [];\n\n  lines.push(`Session: ${details.name}`);\n  lines.push(`ID: ${details.id}`);\n  if (details.description) {\n    lines.push(`Description: ${details.description}`);\n  }\n  lines.push(`Status: ${details.status}`);\n  lines.push(`Query File: ${details.queryFile}`);\n  lines.push(`Created: ${new Date(details.createdAt).toLocaleString()}`);\n  lines.push(`Updated: ${new Date(details.updatedAt).toLocaleString()}`);\n  lines.push('');\n  lines.push(`Total: ${details.totalRetrieved}/${details.totalHits} results`);\n  lines.push('');\n  lines.push('Databases:');\n\n  for (const db of details.databases) {\n    const statusIcon = getStatusIcon(db.status);\n    let line = `  ${statusIcon} ${db.provider.padEnd(10)} ${db.status.padEnd(12)} ${db.retrievedCount}/${db.totalHits}`;\n    if (db.error) {\n      line += ` (${db.error})`;\n    }\n    lines.push(line);\n  }\n\n  return lines.join('\\n');\n}\n\nfunction getStatusIcon(status: string): string {\n  switch (status) {\n    case 'completed':\n      return '\\u2713'; 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package/dist/cli/e2e-helpers.d.ts

@@ -0,0 +1,165 @@
+import { QueryAST } from '../query/types.js';
+import { ProviderConfig } from '../config/schema.js';
+/**
+ * Partial provider configuration for testing.
+ * All fields are optional to allow minimal test configs.
+ */
+export type PartialProviderConfig = Partial<ProviderConfig>;
+/**
+ * Partial config type for creating test configurations.
+ * All fields are optional to allow minimal test configs.
+ */
+export interface PartialConfig {
+    session?: {
+        directory?: string;
+    };
+    log?: {
+        level?: 'debug' | 'info' | 'warn' | 'error';
+    };
+    output?: {
+        color?: boolean;
+        progress_bar?: boolean;
+    };
+    providers?: Partial<Record<string, PartialProviderConfig>>;
+    integration?: {
+        reference_manager?: {
+            enabled?: boolean;
+            command?: string;
+            auto_register?: boolean;
+            with_abstracts?: boolean;
+        };
+    };
+}
+/**
+ * Result of CLI execution
+ */
+export interface ExecResult {
+    stdout: string;
+    stderr: string;
+    exitCode: number;
+}
+/**
+ * Options for CLI execution
+ */
+export interface ExecOptions {
+    /** Environment variables to set */
+    env?: Record<string, string>;
+    /** Working directory */
+    cwd?: string;
+    /** Timeout in milliseconds (default: 30000) */
+    timeout?: number;
+    /** Input to pass to stdin */
+    input?: string;
+}
+/**
+ * E2E test context containing temp directories and cleanup
+ */
+export interface E2EContext {
+    /** Root temp directory for this test */
+    tempDir: string;
+    /** Sessions directory */
+    sessionsDir: string;
+    /** Path to config file */
+    configPath: string;
+    /** Clean up all test artifacts */
+    cleanup: () => Promise<void>;
+}
+/**
+ * Create a temporary directory for E2E tests.
+ * Returns a unique directory path that can be cleaned up later.
+ */
+export declare function createTempDir(): Promise<string>;
+/**
+ * Set up a complete E2E test context with temp dirs and config.
+ * Call cleanup() after tests to remove all artifacts.
+ */
+export declare function setupE2EContext(): Promise<E2EContext>;
+/**
+ * Execute CLI command as a subprocess.
+ * Returns stdout, stderr, and exit code.
+ */
+export declare function execCli(args: string[], options?: ExecOptions): Promise<ExecResult>;
+/**
+ * Create a query YAML file from a QueryAST object.
+ * Returns the path to the created file.
+ */
+export declare function createQueryFile(tempDir: string, query: QueryAST, filename?: string): Promise<string>;
+/**
+ * Create a raw YAML query file from string content.
+ * Useful for testing invalid queries.
+ */
+export declare function createRawQueryFile(tempDir: string, content: string, filename?: string): Promise<string>;
+/**
+ * Create a config TOML file.
+ * Returns the path to the created file.
+ */
+export declare function createConfig(tempDir: string, config: PartialConfig, filename?: string): Promise<string>;
+/**
+ * Create a raw TOML config file from string content.
+ * Useful for testing invalid configs.
+ */
+export declare function createRawConfig(tempDir: string, content: string, filename?: string): Promise<string>;
+/**
+ * Create a simple test query for use in E2E tests.
+ * This is a minimal valid query that can be used across all providers.
+ */
+export declare function createSimpleQuery(name?: string): QueryAST;
+/**
+ * Sample query fixtures for different test scenarios
+ */
+export declare const queryFixtures: {
+    /** Simple single-block query */
+    simple: QueryAST;
+    /** Multi-block query with filters */
+    multiBlock: {
+        name: string;
+        description: string;
+        blocks: ({
+            field: "title_abstract";
+            terms: {
+                keywords: string[];
+            };
+            operator: "AND";
+        } | {
+            field: "keyword";
+            terms: {
+                keywords: string[];
+            };
+            operator: "OR";
+        })[];
+        filters: {
+            yearFrom: number;
+            yearTo: number;
+            languages: string[];
+        };
+        overrides: {};
+    };
+    /** Query with MeSH terms (PubMed-specific) */
+    withMesh: {
+        name: string;
+        blocks: {
+            field: "title_abstract";
+            terms: {
+                keywords: string[];
+                mesh: string[];
+            };
+            operator: "AND";
+        }[];
+        filters: {};
+        overrides: {};
+    };
+};
+/**
+ * Invalid query fixtures for error testing
+ */
+export declare const invalidQueryFixtures: {
+    /** Missing required name field */
+    missingName: string;
+    /** Invalid field type */
+    invalidField: string;
+    /** Empty keywords */
+    emptyKeywords: string;
+    /** Malformed YAML */
+    malformedYaml: string;
+};
+//# sourceMappingURL=e2e-helpers.d.ts.map

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

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package/dist/cli/exit-codes.d.ts

@@ -0,0 +1,25 @@
+/**
+ * CLI Exit Codes
+ *
+ * These codes indicate the type of error that occurred.
+ */
+export declare const EXIT_CODES: {
+    /** Operation completed successfully */
+    readonly SUCCESS: 0;
+    /** General/unexpected error */
+    readonly GENERAL_ERROR: 1;
+    /** Configuration error (missing config, invalid config, etc.) */
+    readonly CONFIG_ERROR: 2;
+    /** Query validation error (invalid YAML, invalid query syntax) */
+    readonly QUERY_ERROR: 3;
+    /** Network/API error (connection failure, API rate limit, etc.) */
+    readonly NETWORK_ERROR: 4;
+    /** Session error (session not found, invalid session state, etc.) */
+    readonly SESSION_ERROR: 5;
+};
+export type ExitCode = (typeof EXIT_CODES)[keyof typeof EXIT_CODES];
+/**
+ * Exit code descriptions for help output.
+ */
+export declare const EXIT_CODE_DESCRIPTIONS: Record<ExitCode, string>;
+//# sourceMappingURL=exit-codes.d.ts.map

package/dist/cli/exit-codes.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/exit-codes.js

@@ -0,0 +1,18 @@
+const EXIT_CODES = {
+  /** Operation completed successfully */
+  SUCCESS: 0,
+  /** General/unexpected error */
+  GENERAL_ERROR: 1,
+  /** Configuration error (missing config, invalid config, etc.) */
+  CONFIG_ERROR: 2,
+  /** Query validation error (invalid YAML, invalid query syntax) */
+  QUERY_ERROR: 3,
+  /** Network/API error (connection failure, API rate limit, etc.) */
+  NETWORK_ERROR: 4,
+  /** Session error (session not found, invalid session state, etc.) */
+  SESSION_ERROR: 5
+};
+export {
+  EXIT_CODES
+};
+//# sourceMappingURL=exit-codes.js.map

package/dist/cli/exit-codes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"exit-codes.js","sources":["../../src/cli/exit-codes.ts"],"sourcesContent":["/**\n * CLI Exit Codes\n *\n * These codes indicate the type of error that occurred.\n */\nexport const EXIT_CODES = {\n  /** Operation completed successfully */\n  SUCCESS: 0,\n  /** General/unexpected error */\n  GENERAL_ERROR: 1,\n  /** Configuration error (missing config, invalid config, etc.) */\n  CONFIG_ERROR: 2,\n  /** Query validation error (invalid YAML, invalid query syntax) */\n  QUERY_ERROR: 3,\n  /** Network/API error (connection failure, API rate limit, etc.) */\n  NETWORK_ERROR: 4,\n  /** Session error (session not found, invalid session state, etc.) */\n  SESSION_ERROR: 5,\n} as const;\n\nexport type ExitCode = (typeof EXIT_CODES)[keyof typeof EXIT_CODES];\n\n/**\n * Exit code descriptions for help output.\n */\nexport const EXIT_CODE_DESCRIPTIONS: Record<ExitCode, string> = {\n  [EXIT_CODES.SUCCESS]: 'Success',\n  [EXIT_CODES.GENERAL_ERROR]: 'General error',\n  [EXIT_CODES.CONFIG_ERROR]: 'Configuration error',\n  [EXIT_CODES.QUERY_ERROR]: 'Query validation error',\n  [EXIT_CODES.NETWORK_ERROR]: 'Network/API error',\n  [EXIT_CODES.SESSION_ERROR]: 'Session error',\n};\n"],"names":[],"mappings":"AAKO,MAAM,aAAa;AAAA;AAAA,EAExB,SAAS;AAAA;AAAA,EAET,eAAe;AAAA;AAAA,EAEf,cAAc;AAAA;AAAA,EAEd,aAAa;AAAA;AAAA,EAEb,eAAe;AAAA;AAAA,EAEf,eAAe;AACjB;"}

package/dist/cli/index.d.ts

@@ -0,0 +1,25 @@
+import { Command } from 'commander';
+/**
+ * Global CLI options available to all commands.
+ */
+export interface GlobalOptions {
+    /** Path to config file */
+    config?: string;
+    /** Path to session directory */
+    sessionDir?: string;
+    /** Enable verbose output */
+    verbose: boolean;
+    /** Suppress all output except errors */
+    quiet: boolean;
+    /** Enable color output (default: true, use --no-color to disable) */
+    color: boolean;
+}
+/**
+ * Create and configure the CLI program.
+ */
+export declare function createProgram(): Command;
+/**
+ * Main entry point for CLI execution.
+ */
+export declare function main(): Promise<void>;
+//# sourceMappingURL=index.d.ts.map

package/dist/cli/index.d.ts.map

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