@ncukondo/search-hub 0.1.0

package/dist/cli/commands/init.js

@@ -0,0 +1,134 @@
+import { mkdir, writeFile, access, constants } from "node:fs/promises";
+import { join } from "node:path";
+import { stringify } from "@iarna/toml";
+import "../../config/schema.js";
+import { getDefaultConfig } from "../../config/defaults.js";
+import { getConfigDir, getDataDir } from "../../config/paths.js";
+import "node:os";
+async function exists(path) {
+  try {
+    await access(path, constants.F_OK);
+    return true;
+  } catch {
+    return false;
+  }
+}
+function configToToml(config) {
+  return {
+    session: {
+      directory: config.session.directory
+    },
+    log: {
+      level: config.log.level
+    },
+    output: {
+      color: config.output.color,
+      progress_bar: config.output.progress_bar
+    },
+    providers: {
+      pubmed: {
+        enabled: config.providers.pubmed.enabled,
+        api_key: config.providers.pubmed.api_key ?? "",
+        email: config.providers.pubmed.email ?? "",
+        rate_limit: config.providers.pubmed.rate_limit,
+        timeout: config.providers.pubmed.timeout,
+        retries: config.providers.pubmed.retries,
+        max_results: config.providers.pubmed.max_results
+      },
+      eric: {
+        enabled: config.providers.eric.enabled,
+        rate_limit: config.providers.eric.rate_limit,
+        timeout: config.providers.eric.timeout,
+        retries: config.providers.eric.retries,
+        max_results: config.providers.eric.max_results
+      },
+      arxiv: {
+        enabled: config.providers.arxiv.enabled,
+        rate_limit: config.providers.arxiv.rate_limit,
+        timeout: config.providers.arxiv.timeout,
+        retries: config.providers.arxiv.retries,
+        max_results: config.providers.arxiv.max_results
+      },
+      scopus: {
+        enabled: config.providers.scopus.enabled,
+        api_key: config.providers.scopus.api_key ?? "",
+        inst_token: config.providers.scopus.inst_token ?? "",
+        rate_limit: config.providers.scopus.rate_limit,
+        timeout: config.providers.scopus.timeout,
+        retries: config.providers.scopus.retries,
+        max_results: config.providers.scopus.max_results
+      },
+      wos: {
+        enabled: config.providers.wos.enabled,
+        api_key: config.providers.wos.api_key ?? "",
+        rate_limit: config.providers.wos.rate_limit,
+        timeout: config.providers.wos.timeout,
+        retries: config.providers.wos.retries,
+        max_results: config.providers.wos.max_results
+      },
+      embase: {
+        enabled: config.providers.embase.enabled,
+        rate_limit: config.providers.embase.rate_limit,
+        timeout: config.providers.embase.timeout,
+        retries: config.providers.embase.retries,
+        max_results: config.providers.embase.max_results
+      }
+    },
+    integration: {
+      reference_manager: {
+        enabled: config.integration.reference_manager.enabled,
+        command: config.integration.reference_manager.command,
+        auto_register: config.integration.reference_manager.auto_register
+      }
+    }
+  };
+}
+function generateConfigContent(config) {
+  const tomlObj = configToToml(config);
+  const header = `# search-hub configuration file
+# See: https://github.com/search-hub/search-hub for documentation
+
+`;
+  return header + stringify(tomlObj);
+}
+async function init(options = {}) {
+  const {
+    configDir = getConfigDir(),
+    dataDir = getDataDir(),
+    force = false
+  } = options;
+  const configPath = join(configDir, "config.toml");
+  const sessionsDir = join(dataDir, "sessions");
+  const result = {
+    success: false,
+    configPath,
+    sessionsDir,
+    configDir,
+    dataDir
+  };
+  if (await exists(configDir)) {
+    if (!force) {
+      return {
+        ...result,
+        alreadyExists: true,
+        message: `Configuration directory already exists at ${configDir}. Use --force to overwrite.`
+      };
+    }
+    result.overwritten = true;
+  }
+  await mkdir(configDir, { recursive: true });
+  await mkdir(sessionsDir, { recursive: true });
+  const defaultConfig = getDefaultConfig();
+  defaultConfig.session.directory = sessionsDir;
+  const configContent = generateConfigContent(defaultConfig);
+  await writeFile(configPath, configContent, "utf-8");
+  return {
+    ...result,
+    success: true,
+    message: result.overwritten ? `Configuration overwritten at ${configDir}` : `Configuration created at ${configDir}`
+  };
+}
+export {
+  init
+};
+//# sourceMappingURL=init.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"init.js","sources":["../../../src/cli/commands/init.ts"],"sourcesContent":["import { mkdir, writeFile, access, constants } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { stringify as stringifyToml } from '@iarna/toml';\nimport { getDefaultConfig } from '../../config/index.js';\nimport { getConfigDir, getDataDir } from '../../config/paths.js';\nimport type { Config } from '../../config/index.js';\n\n/**\n * Options for the init command.\n */\nexport interface InitOptions {\n  /** Config directory (defaults to platform-specific via getConfigDir()) */\n  configDir?: string;\n  /** Data directory (defaults to platform-specific via getDataDir()) */\n  dataDir?: string;\n  /** Force overwrite if directory already exists */\n  force?: boolean;\n}\n\n/**\n * Result of the init command.\n */\nexport interface InitResult {\n  /** Whether initialization was successful */\n  success: boolean;\n  /** Path to the created config file */\n  configPath: string;\n  /** Path to the sessions directory */\n  sessionsDir: string;\n  /** Path to the config directory */\n  configDir: string;\n  /** Path to the data directory */\n  dataDir: string;\n  /** Whether files already existed (only when success=false) */\n  alreadyExists?: boolean;\n  /** Whether existing files were overwritten (only when force=true) */\n  overwritten?: boolean;\n  /** Message describing the result */\n  message?: string;\n}\n\n/**\n * Check if a file or directory exists.\n */\nasync function exists(path: string): Promise<boolean> {\n  try {\n    await access(path, constants.F_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Convert Config to TOML-compatible object.\n * Removes undefined values and converts to the expected format.\n */\nfunction configToToml(config: Config): Record<string, unknown> {\n  return {\n    session: {\n      directory: config.session.directory,\n    },\n    log: {\n      level: config.log.level,\n    },\n    output: {\n      color: config.output.color,\n      progress_bar: config.output.progress_bar,\n    },\n    providers: {\n      pubmed: {\n        enabled: config.providers.pubmed.enabled,\n        api_key: config.providers.pubmed.api_key ?? '',\n        email: config.providers.pubmed.email ?? '',\n        rate_limit: config.providers.pubmed.rate_limit,\n        timeout: config.providers.pubmed.timeout,\n        retries: config.providers.pubmed.retries,\n        max_results: config.providers.pubmed.max_results,\n      },\n      eric: {\n        enabled: config.providers.eric.enabled,\n        rate_limit: config.providers.eric.rate_limit,\n        timeout: config.providers.eric.timeout,\n        retries: config.providers.eric.retries,\n        max_results: config.providers.eric.max_results,\n      },\n      arxiv: {\n        enabled: config.providers.arxiv.enabled,\n        rate_limit: config.providers.arxiv.rate_limit,\n        timeout: config.providers.arxiv.timeout,\n        retries: config.providers.arxiv.retries,\n        max_results: config.providers.arxiv.max_results,\n      },\n      scopus: {\n        enabled: config.providers.scopus.enabled,\n        api_key: config.providers.scopus.api_key ?? '',\n        inst_token: config.providers.scopus.inst_token ?? '',\n        rate_limit: config.providers.scopus.rate_limit,\n        timeout: config.providers.scopus.timeout,\n        retries: config.providers.scopus.retries,\n        max_results: config.providers.scopus.max_results,\n      },\n      wos: {\n        enabled: config.providers.wos.enabled,\n        api_key: config.providers.wos.api_key ?? '',\n        rate_limit: config.providers.wos.rate_limit,\n        timeout: config.providers.wos.timeout,\n        retries: config.providers.wos.retries,\n        max_results: config.providers.wos.max_results,\n      },\n      embase: {\n        enabled: config.providers.embase.enabled,\n        rate_limit: config.providers.embase.rate_limit,\n        timeout: config.providers.embase.timeout,\n        retries: config.providers.embase.retries,\n        max_results: config.providers.embase.max_results,\n      },\n    },\n    integration: {\n      reference_manager: {\n        enabled: config.integration.reference_manager.enabled,\n        command: config.integration.reference_manager.command,\n        auto_register: config.integration.reference_manager.auto_register,\n      },\n    },\n  };\n}\n\n/**\n * Generate TOML config file content with comments.\n */\nfunction generateConfigContent(config: Config): string {\n  const tomlObj = configToToml(config);\n  const header = `# search-hub configuration file\n# See: https://github.com/search-hub/search-hub for documentation\n\n`;\n  return header + stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n}\n\n/**\n * Initialize the search-hub configuration directory.\n *\n * Creates:\n * - Config directory with config.toml\n * - Data directory with sessions/ subdirectory\n *\n * On Linux (XDG):\n * - ~/.config/search-hub/config.toml\n * - ~/.local/share/search-hub/sessions/\n */\nexport async function init(options: InitOptions = {}): Promise<InitResult> {\n  const {\n    configDir = getConfigDir(),\n    dataDir = getDataDir(),\n    force = false,\n  } = options;\n\n  const configPath = join(configDir, 'config.toml');\n  const sessionsDir = join(dataDir, 'sessions');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\n    sessionsDir,\n    configDir,\n    dataDir,\n  };\n\n  // Check if config directory already exists\n  if (await exists(configDir)) {\n    if (!force) {\n      return {\n        ...result,\n        alreadyExists: true,\n        message: `Configuration directory already exists at ${configDir}. Use --force to overwrite.`,\n      };\n    }\n    result.overwritten = true;\n  }\n\n  // Create directories\n  await mkdir(configDir, { recursive: true });\n  await mkdir(sessionsDir, { recursive: true });\n\n  // Generate and write config file\n  // Use the default sessions directory for the saved config\n  const defaultConfig = getDefaultConfig();\n  // Set session.directory to the actual sessions path for the config file\n  defaultConfig.session.directory = sessionsDir;\n  const configContent = generateConfigContent(defaultConfig);\n  await writeFile(configPath, configContent, 'utf-8');\n\n  return {\n    ...result,\n    success: true,\n    message: result.overwritten\n      ? `Configuration overwritten at ${configDir}`\n      : `Configuration created at ${configDir}`,\n  };\n}\n"],"names":["stringifyToml"],"mappings":";;;;;;;AA4CA,eAAe,OAAO,MAAgC;AACpD,MAAI;AACF,UAAM,OAAO,MAAM,UAAU,IAAI;AACjC,WAAO;AAAA,EACT,QAAQ;AACN,WAAO;AAAA,EACT;AACF;AAMA,SAAS,aAAa,QAAyC;AAC7D,SAAO;AAAA,IACL,SAAS;AAAA,MACP,WAAW,OAAO,QAAQ;AAAA,IAAA;AAAA,IAE5B,KAAK;AAAA,MACH,OAAO,OAAO,IAAI;AAAA,IAAA;AAAA,IAEpB,QAAQ;AAAA,MACN,OAAO,OAAO,OAAO;AAAA,MACrB,cAAc,OAAO,OAAO;AAAA,IAAA;AAAA,IAE9B,WAAW;AAAA,MACT,QAAQ;AAAA,QACN,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,SAAS,OAAO,UAAU,OAAO,WAAW;AAAA,QAC5C,OAAO,OAAO,UAAU,OAAO,SAAS;AAAA,QACxC,YAAY,OAAO,UAAU,OAAO;AAAA,QACpC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,aAAa,OAAO,UAAU,OAAO;AAAA,MAAA;AAAA,MAEvC,MAAM;AAAA,QACJ,SAAS,OAAO,UAAU,KAAK;AAAA,QAC/B,YAAY,OAAO,UAAU,KAAK;AAAA,QAClC,SAAS,OAAO,UAAU,KAAK;AAAA,QAC/B,SAAS,OAAO,UAAU,KAAK;AAAA,QAC/B,aAAa,OAAO,UAAU,KAAK;AAAA,MAAA;AAAA,MAErC,OAAO;AAAA,QACL,SAAS,OAAO,UAAU,MAAM;AAAA,QAChC,YAAY,OAAO,UAAU,MAAM;AAAA,QACnC,SAAS,OAAO,UAAU,MAAM;AAAA,QAChC,SAAS,OAAO,UAAU,MAAM;AAAA,QAChC,aAAa,OAAO,UAAU,MAAM;AAAA,MAAA;AAAA,MAEtC,QAAQ;AAAA,QACN,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,SAAS,OAAO,UAAU,OAAO,WAAW;AAAA,QAC5C,YAAY,OAAO,UAAU,OAAO,cAAc;AAAA,QAClD,YAAY,OAAO,UAAU,OAAO;AAAA,QACpC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,aAAa,OAAO,UAAU,OAAO;AAAA,MAAA;AAAA,MAEvC,KAAK;AAAA,QACH,SAAS,OAAO,UAAU,IAAI;AAAA,QAC9B,SAAS,OAAO,UAAU,IAAI,WAAW;AAAA,QACzC,YAAY,OAAO,UAAU,IAAI;AAAA,QACjC,SAAS,OAAO,UAAU,IAAI;AAAA,QAC9B,SAAS,OAAO,UAAU,IAAI;AAAA,QAC9B,aAAa,OAAO,UAAU,IAAI;AAAA,MAAA;AAAA,MAEpC,QAAQ;AAAA,QACN,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,YAAY,OAAO,UAAU,OAAO;AAAA,QACpC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,SAAS,OAAO,UAAU,OAAO;AAAA,QACjC,aAAa,OAAO,UAAU,OAAO;AAAA,MAAA;AAAA,IACvC;AAAA,IAEF,aAAa;AAAA,MACX,mBAAmB;AAAA,QACjB,SAAS,OAAO,YAAY,kBAAkB;AAAA,QAC9C,SAAS,OAAO,YAAY,kBAAkB;AAAA,QAC9C,eAAe,OAAO,YAAY,kBAAkB;AAAA,MAAA;AAAA,IACtD;AAAA,EACF;AAEJ;AAKA,SAAS,sBAAsB,QAAwB;AACrD,QAAM,UAAU,aAAa,MAAM;AACnC,QAAM,SAAS;AAAA;AAAA;AAAA;AAIf,SAAO,SAASA,UAAc,OAA8C;AAC9E;AAaA,eAAsB,KAAK,UAAuB,IAAyB;AACzE,QAAM;AAAA,IACJ,YAAY,aAAA;AAAA,IACZ,UAAU,WAAA;AAAA,IACV,QAAQ;AAAA,EAAA,IACN;AAEJ,QAAM,aAAa,KAAK,WAAW,aAAa;AAChD,QAAM,cAAc,KAAK,SAAS,UAAU;AAE5C,QAAM,SAAqB;AAAA,IACzB,SAAS;AAAA,IACT;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EAAA;AAIF,MAAI,MAAM,OAAO,SAAS,GAAG;AAC3B,QAAI,CAAC,OAAO;AACV,aAAO;AAAA,QACL,GAAG;AAAA,QACH,eAAe;AAAA,QACf,SAAS,6CAA6C,SAAS;AAAA,MAAA;AAAA,IAEnE;AACA,WAAO,cAAc;AAAA,EACvB;AAGA,QAAM,MAAM,WAAW,EAAE,WAAW,MAAM;AAC1C,QAAM,MAAM,aAAa,EAAE,WAAW,MAAM;AAI5C,QAAM,gBAAgB,iBAAA;AAEtB,gBAAc,QAAQ,YAAY;AAClC,QAAM,gBAAgB,sBAAsB,aAAa;AACzD,QAAM,UAAU,YAAY,eAAe,OAAO;AAElD,SAAO;AAAA,IACL,GAAG;AAAA,IACH,SAAS;AAAA,IACT,SAAS,OAAO,cACZ,gCAAgC,SAAS,KACzC,4BAA4B,SAAS;AAAA,EAAA;AAE7C;"}

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

@@ -0,0 +1,32 @@
+import { TranslatedQuery, ProviderName } from '../../../providers/base/types.js';
+/**
+ * Options for translate command.
+ */
+export interface TranslateOptions {
+    /** Specific providers to translate for */
+    providers?: ProviderName[];
+}
+/**
+ * Result of query translation.
+ */
+export interface TranslateResult {
+    /** Whether translation succeeded */
+    success: boolean;
+    /** Error message if failed */
+    error?: string;
+    /** Translations by provider name */
+    translations?: Record<string, TranslatedQuery>;
+}
+/**
+ * Translate a query YAML file to native syntax for each provider.
+ *
+ * @param filePath - Path to the query file
+ * @param options - Translation options
+ * @returns Translation result
+ */
+export declare function translateQueryCommand(filePath: string, options?: TranslateOptions): Promise<TranslateResult>;
+/**
+ * Format translation result for display.
+ */
+export declare function formatTranslateResult(result: TranslateResult, filePath: string): string;
+//# sourceMappingURL=translate.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/cli/commands/query/translate.js

@@ -0,0 +1,76 @@
+import { readFile } from "node:fs/promises";
+import { parseQueryString } from "../../../query/parser.js";
+import "../../../query/validator.js";
+import { translateQuery as translateQuery$3 } from "../../../providers/pubmed/translator.js";
+import { translateQuery as translateQuery$2 } from "../../../providers/eric/translator.js";
+import { translateQuery as translateQuery$1 } from "../../../providers/arxiv/translator.js";
+import { translateQuery } from "../../../providers/scopus/translator.js";
+const translators = {
+  pubmed: translateQuery$3,
+  eric: translateQuery$2,
+  arxiv: translateQuery$1,
+  scopus: translateQuery
+};
+const DEFAULT_PROVIDERS = ["pubmed", "eric", "arxiv", "scopus"];
+async function translateQueryCommand(filePath, options = {}) {
+  let content;
+  try {
+    content = await readFile(filePath, "utf-8");
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Failed to read file";
+    return {
+      success: false,
+      error: message
+    };
+  }
+  let ast;
+  try {
+    ast = parseQueryString(content);
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Failed to parse query file";
+    return {
+      success: false,
+      error: message
+    };
+  }
+  const providers = options.providers ?? DEFAULT_PROVIDERS;
+  const translations = {};
+  for (const provider of providers) {
+    const translator = translators[provider];
+    if (translator) {
+      try {
+        translations[provider] = translator(ast);
+      } catch (error) {
+        const message = error instanceof Error ? error.message : `Failed to translate for ${provider}`;
+        return {
+          success: false,
+          error: `${provider}: ${message}`
+        };
+      }
+    }
+  }
+  return {
+    success: true,
+    translations
+  };
+}
+function formatTranslateResult(result, filePath) {
+  if (!result.success) {
+    return `✗ Failed to translate: ${filePath}
+  Error: ${result.error}`;
+  }
+  const lines = [`Translations for: ${filePath}`, ""];
+  if (result.translations) {
+    for (const [provider, translation] of Object.entries(result.translations)) {
+      lines.push(`[${provider.toUpperCase()}]`);
+      lines.push(translation.native);
+      lines.push("");
+    }
+  }
+  return lines.join("\n");
+}
+export {
+  formatTranslateResult,
+  translateQueryCommand
+};
+//# sourceMappingURL=translate.js.map

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

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

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

@@ -0,0 +1,25 @@
+/**
+ * Result of query validation.
+ */
+export interface ValidateResult {
+    /** Whether validation succeeded */
+    success: boolean;
+    /** Error messages if validation failed */
+    errors?: string[];
+    /** Query name (if valid) */
+    queryName?: string;
+    /** Number of query blocks (if valid) */
+    blockCount?: number;
+}
+/**
+ * Validate a query YAML file.
+ *
+ * @param filePath - Path to the query file
+ * @returns Validation result
+ */
+export declare function validateQueryCommand(filePath: string): Promise<ValidateResult>;
+/**
+ * Format validation result for display.
+ */
+export declare function formatValidateResult(result: ValidateResult, filePath: string): string;
+//# sourceMappingURL=validate.d.ts.map

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

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

@@ -0,0 +1,68 @@
+import { readFile } from "node:fs/promises";
+import { parseQueryString } from "../../../query/parser.js";
+import { ValidationError } from "../../../query/validator.js";
+import { ZodError } from "zod";
+async function validateQueryCommand(filePath) {
+  let content;
+  try {
+    content = await readFile(filePath, "utf-8");
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Failed to read file";
+    return {
+      success: false,
+      errors: [message]
+    };
+  }
+  try {
+    const ast = parseQueryString(content);
+    return {
+      success: true,
+      queryName: ast.name,
+      blockCount: ast.blocks.length
+    };
+  } catch (error) {
+    if (error instanceof ZodError) {
+      const errors = error.issues.map((e) => {
+        const path = e.path.join(".");
+        return path ? `${path}: ${e.message}` : e.message;
+      });
+      return {
+        success: false,
+        errors
+      };
+    }
+    if (error instanceof ValidationError) {
+      return {
+        success: false,
+        errors: [error.message]
+      };
+    }
+    const message = error instanceof Error ? error.message : "Unknown validation error";
+    return {
+      success: false,
+      errors: [message]
+    };
+  }
+}
+function formatValidateResult(result, filePath) {
+  if (result.success) {
+    const lines2 = [
+      `✓ Valid query file: ${filePath}`,
+      `  Name: ${result.queryName}`,
+      `  Blocks: ${result.blockCount}`
+    ];
+    return lines2.join("\n");
+  }
+  const lines = [`✗ Invalid query file: ${filePath}`, "", "Errors:"];
+  if (result.errors) {
+    for (const error of result.errors) {
+      lines.push(`  - ${error}`);
+    }
+  }
+  return lines.join("\n");
+}
+export {
+  formatValidateResult,
+  validateQueryCommand
+};
+//# sourceMappingURL=validate.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"validate.js","sources":["../../../../src/cli/commands/query/validate.ts"],"sourcesContent":["/**\n * Query validate command implementation.\n *\n * Validates a YAML query file and reports any errors.\n */\nimport { readFile } from 'node:fs/promises';\nimport { parseQueryString, ValidationError } from '../../../query/index.js';\nimport { ZodError } from 'zod';\n\n/**\n * Result of query validation.\n */\nexport interface ValidateResult {\n  /** Whether validation succeeded */\n  success: boolean;\n  /** Error messages if validation failed */\n  errors?: string[];\n  /** Query name (if valid) */\n  queryName?: string;\n  /** Number of query blocks (if valid) */\n  blockCount?: number;\n}\n\n/**\n * Validate a query YAML file.\n *\n * @param filePath - Path to the query file\n * @returns Validation result\n */\nexport async function validateQueryCommand(\n  filePath: string\n): Promise<ValidateResult> {\n  // Read file\n  let content: string;\n  try {\n    content = await readFile(filePath, 'utf-8');\n  } catch (error) {\n    const message =\n      error instanceof Error ? error.message : 'Failed to read file';\n    return {\n      success: false,\n      errors: [message],\n    };\n  }\n\n  // Parse and validate using query module\n  try {\n    const ast = parseQueryString(content);\n    return {\n      success: true,\n      queryName: ast.name,\n      blockCount: ast.blocks.length,\n    };\n  } catch (error) {\n    if (error instanceof ZodError) {\n      const errors = error.issues.map((e) => {\n        const path = e.path.join('.');\n        return path ? `${path}: ${e.message}` : e.message;\n      });\n      return {\n        success: false,\n        errors,\n      };\n    }\n\n    if (error instanceof ValidationError) {\n      return {\n        success: false,\n        errors: [error.message],\n      };\n    }\n\n    // YAML parse error or other error\n    const message =\n      error instanceof Error ? error.message : 'Unknown validation error';\n    return {\n      success: false,\n      errors: [message],\n    };\n  }\n}\n\n/**\n * Format validation result for display.\n */\nexport function formatValidateResult(\n  result: ValidateResult,\n  filePath: string\n): string {\n  if (result.success) {\n    const lines = [\n      `✓ Valid query file: ${filePath}`,\n      `  Name: ${result.queryName}`,\n      `  Blocks: ${result.blockCount}`,\n    ];\n    return lines.join('\\n');\n  }\n\n  const lines = [`✗ Invalid query file: ${filePath}`, '', 'Errors:'];\n  if (result.errors) {\n    for (const error of result.errors) {\n      lines.push(`  - ${error}`);\n    }\n  }\n  return lines.join('\\n');\n}\n"],"names":["lines"],"mappings":";;;;AA6BA,eAAsB,qBACpB,UACyB;AAEzB,MAAI;AACJ,MAAI;AACF,cAAU,MAAM,SAAS,UAAU,OAAO;AAAA,EAC5C,SAAS,OAAO;AACd,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,QAAQ,CAAC,OAAO;AAAA,IAAA;AAAA,EAEpB;AAGA,MAAI;AACF,UAAM,MAAM,iBAAiB,OAAO;AACpC,WAAO;AAAA,MACL,SAAS;AAAA,MACT,WAAW,IAAI;AAAA,MACf,YAAY,IAAI,OAAO;AAAA,IAAA;AAAA,EAE3B,SAAS,OAAO;AACd,QAAI,iBAAiB,UAAU;AAC7B,YAAM,SAAS,MAAM,OAAO,IAAI,CAAC,MAAM;AACrC,cAAM,OAAO,EAAE,KAAK,KAAK,GAAG;AAC5B,eAAO,OAAO,GAAG,IAAI,KAAK,EAAE,OAAO,KAAK,EAAE;AAAA,MAC5C,CAAC;AACD,aAAO;AAAA,QACL,SAAS;AAAA,QACT;AAAA,MAAA;AAAA,IAEJ;AAEA,QAAI,iBAAiB,iBAAiB;AACpC,aAAO;AAAA,QACL,SAAS;AAAA,QACT,QAAQ,CAAC,MAAM,OAAO;AAAA,MAAA;AAAA,IAE1B;AAGA,UAAM,UACJ,iBAAiB,QAAQ,MAAM,UAAU;AAC3C,WAAO;AAAA,MACL,SAAS;AAAA,MACT,QAAQ,CAAC,OAAO;AAAA,IAAA;AAAA,EAEpB;AACF;AAKO,SAAS,qBACd,QACA,UACQ;AACR,MAAI,OAAO,SAAS;AAClB,UAAMA,SAAQ;AAAA,MACZ,uBAAuB,QAAQ;AAAA,MAC/B,WAAW,OAAO,SAAS;AAAA,MAC3B,aAAa,OAAO,UAAU;AAAA,IAAA;AAEhC,WAAOA,OAAM,KAAK,IAAI;AAAA,EACxB;AAEA,QAAM,QAAQ,CAAC,yBAAyB,QAAQ,IAAI,IAAI,SAAS;AACjE,MAAI,OAAO,QAAQ;AACjB,eAAW,SAAS,OAAO,QAAQ;AACjC,YAAM,KAAK,OAAO,KAAK,EAAE;AAAA,IAC3B;AAAA,EACF;AACA,SAAO,MAAM,KAAK,IAAI;AACxB;"}

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

@@ -0,0 +1,39 @@
+import { ProviderName, Article } from '../../providers/base/types.js';
+export interface RegisterCommandOptions {
+    sessionId: string;
+    providers?: ProviderName[];
+    dryRun: boolean;
+    withAbstracts: boolean;
+}
+export interface CommandLineOptions {
+    db?: string | undefined;
+    dryRun?: boolean | undefined;
+    withAbstracts?: boolean | undefined;
+}
+export interface ValidationResult {
+    valid: boolean;
+    error?: string;
+}
+/**
+ * Parse command line options into RegisterCommandOptions.
+ */
+export declare function parseRegisterOptions(sessionId: string, options: CommandLineOptions): RegisterCommandOptions;
+/**
+ * Validate register command input.
+ */
+export declare function validateRegisterInput(options: RegisterCommandOptions): ValidationResult;
+/**
+ * Format registration summary for CLI output.
+ */
+export declare function formatRegistrationSummary(summary: {
+    total: number;
+    added: number;
+    skipped: number;
+    failed: number;
+    noId: number;
+}): string;
+/**
+ * Format dry run output showing what would be registered.
+ */
+export declare function formatDryRunOutput(articles: Article[]): string;
+//# sourceMappingURL=register.d.ts.map

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

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package/dist/cli/commands/register.js

@@ -0,0 +1,78 @@
+import { parseProviderNames } from "../utils/validation.js";
+function parseRegisterOptions(sessionId, options) {
+  const result = {
+    sessionId,
+    dryRun: options.dryRun ?? false,
+    withAbstracts: options.withAbstracts ?? false
+  };
+  if (options.db) {
+    result.providers = parseProviderNames(options.db);
+  }
+  return result;
+}
+function validateRegisterInput(options) {
+  if (!options.sessionId || options.sessionId.trim() === "") {
+    return {
+      valid: false,
+      error: "A session ID is required"
+    };
+  }
+  return { valid: true };
+}
+function formatRegistrationSummary(summary) {
+  const lines = ["Registration complete:"];
+  lines.push(`  ✓ ${summary.added} added`);
+  if (summary.skipped > 0) {
+    lines.push(`  ⚠ ${summary.skipped} duplicates (already in library)`);
+  }
+  if (summary.failed > 0) {
+    lines.push(`  ✗ ${summary.failed} failed`);
+  }
+  if (summary.noId > 0) {
+    lines.push(`  - ${summary.noId} skipped (no identifier)`);
+  }
+  return lines.join("\n");
+}
+function getRegistrationId(article) {
+  if (article.pmid) {
+    return `pmid:${article.pmid}`;
+  }
+  if (article.doi) {
+    return article.doi;
+  }
+  return null;
+}
+function formatDryRunOutput(articles) {
+  const withId = [];
+  const withoutId = [];
+  for (const article of articles) {
+    const id = getRegistrationId(article);
+    if (id) {
+      withId.push({ article, id });
+    } else {
+      withoutId.push(article);
+    }
+  }
+  const lines = [];
+  lines.push(
+    `Would register ${withId.length} reference${withId.length !== 1 ? "s" : ""}:`
+  );
+  for (const { id, article } of withId) {
+    const title = article.title.length > 60 ? article.title.substring(0, 57) + "..." : article.title;
+    lines.push(`  - ${id}: ${title}`);
+  }
+  if (withoutId.length > 0) {
+    lines.push("");
+    lines.push(
+      `${withoutId.length} article${withoutId.length !== 1 ? "s" : ""} will be skipped (no identifier)`
+    );
+  }
+  return lines.join("\n");
+}
+export {
+  formatDryRunOutput,
+  formatRegistrationSummary,
+  parseRegisterOptions,
+  validateRegisterInput
+};
+//# sourceMappingURL=register.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"register.js","sources":["../../../src/cli/commands/register.ts"],"sourcesContent":["/**\n * Register command for reference-manager integration.\n * Registers search results with reference-manager CLI.\n */\n\nimport type { ProviderName } from '../../providers/base/types.js';\nimport type { Article } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\n\nexport interface RegisterCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  dryRun: boolean;\n  withAbstracts: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  dryRun?: boolean | undefined;\n  withAbstracts?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Parse command line options into RegisterCommandOptions.\n */\nexport function parseRegisterOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): RegisterCommandOptions {\n  const result: RegisterCommandOptions = {\n    sessionId,\n    dryRun: options.dryRun ?? false,\n    withAbstracts: options.withAbstracts ?? false,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  return result;\n}\n\n/**\n * Validate register command input.\n */\nexport function validateRegisterInput(options: RegisterCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  return { valid: true };\n}\n\n/**\n * Format registration summary for CLI output.\n */\nexport function formatRegistrationSummary(summary: {\n  total: number;\n  added: number;\n  skipped: number;\n  failed: number;\n  noId: number;\n}): string {\n  const lines: string[] = ['Registration complete:'];\n\n  // Added\n  lines.push(`  ✓ ${summary.added} added`);\n\n  // Duplicates (skipped)\n  if (summary.skipped > 0) {\n    lines.push(`  ⚠ ${summary.skipped} duplicates (already in library)`);\n  }\n\n  // Failed\n  if (summary.failed > 0) {\n    lines.push(`  ✗ ${summary.failed} failed`);\n  }\n\n  // No ID (skipped)\n  if (summary.noId > 0) {\n    lines.push(`  - ${summary.noId} skipped (no identifier)`);\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get registration identifier for an article.\n * PMID is preferred over DOI for better metadata quality.\n */\nfunction getRegistrationId(article: Article): string | null {\n  if (article.pmid) {\n    return `pmid:${article.pmid}`;\n  }\n  if (article.doi) {\n    return article.doi;\n  }\n  return null;\n}\n\n/**\n * Format dry run output showing what would be registered.\n */\nexport function formatDryRunOutput(articles: Article[]): string {\n  const withId: Array<{ article: Article; id: string }> = [];\n  const withoutId: Article[] = [];\n\n  for (const article of articles) {\n    const id = getRegistrationId(article);\n    if (id) {\n      withId.push({ article, id });\n    } else {\n      withoutId.push(article);\n    }\n  }\n\n  const lines: string[] = [];\n\n  // Summary\n  lines.push(\n    `Would register ${withId.length} reference${withId.length !== 1 ? 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package/dist/cli/commands/resume-executor.d.ts

@@ -0,0 +1,19 @@
+import { ResumeCommandOptions } from './resume.js';
+import { Config } from '../../config/index.js';
+/**
+ * Result of a resume execution.
+ */
+export interface ResumeExecutionResult {
+    success: boolean;
+    resumed: number;
+    results?: Record<string, {
+        hits: number;
+        retrieved: number;
+    }>;
+    error?: string;
+}
+/**
+ * Execute resume for interrupted sessions.
+ */
+export declare function executeResume(options: ResumeCommandOptions, sessionsDir: string, config: Config, showProgress?: boolean): Promise<ResumeExecutionResult>;
+//# sourceMappingURL=resume-executor.d.ts.map

package/dist/cli/commands/resume-executor.d.ts.map

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