@ncukondo/search-hub 0.22.0 → 0.23.1

package/dist/cli/commands/init.js

@@ -3,8 +3,27 @@ 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 { getConfigDir, getProjectDir } from "../../config/paths.js";
 import "node:os";
+const FULL_PROVIDERS = ["pubmed", "eric", "arxiv", "scopus"];
+const MINIMAL_PROVIDERS = ["wos", "embase"];
+function buildProvidersToml(config) {
+  const providers = {};
+  for (const name of FULL_PROVIDERS) {
+    const p = config.providers[name];
+    providers[name] = {
+      enabled: p.enabled,
+      rate_limit: p.rate_limit,
+      timeout: p.timeout,
+      retries: p.retries,
+      max_results: p.max_results
+    };
+  }
+  for (const name of MINIMAL_PROVIDERS) {
+    providers[name] = { enabled: config.providers[name].enabled };
+  }
+  return providers;
+}
 async function exists(path) {
   try {
     await access(path, constants.F_OK);
@@ -13,11 +32,20 @@ async function exists(path) {
     return false;
   }
 }
-function configToToml(config) {
+function localConfigToToml(config) {
   return {
-    session: {
-      directory: config.session.directory
-    },
+    providers: buildProvidersToml(config),
+    integration: {
+      reference_manager: {
+        enabled: config.integration.reference_manager.enabled,
+        command: config.integration.reference_manager.command,
+        auto_register: config.integration.reference_manager.auto_register
+      }
+    }
+  };
+}
+function generateGlobalConfigContent(config) {
+  const tomlObj = {
     log: {
       level: config.log.level
     },
@@ -25,55 +53,7 @@ function configToToml(config) {
       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
-      }
-    },
+    providers: buildProvidersToml(config),
     integration: {
       reference_manager: {
         enabled: config.integration.reference_manager.enabled,
@@ -82,54 +62,114 @@ function configToToml(config) {
       }
     }
   };
-}
-function generateConfigContent(config) {
-  const tomlObj = configToToml(config);
-  const header = `# search-hub configuration file
+  const header = `# search-hub global configuration
 # See: https://github.com/search-hub/search-hub for documentation
+#
+# [session]
+# directory = ""  # Override default session directory (empty = platform default)
+
+`;
+  const tomlContent = stringify(tomlObj);
+  const lines = tomlContent.split("\n");
+  const result = [];
+  for (const line of lines) {
+    result.push(line);
+    if (line.startsWith("[providers.pubmed]")) {
+      result.push('# api_key = ""    # Optional but recommended (NCBI E-utilities)');
+      result.push('# email = ""      # Required by NCBI for tracking');
+    } else if (line.startsWith("[providers.scopus]")) {
+      result.push('# api_key = ""    # Required for Scopus access');
+      result.push('# inst_token = "" # Optional institutional token');
+    } else if (line.startsWith("[providers.wos]")) {
+      result.push('# api_key = ""    # Required for Web of Science');
+    }
+  }
+  return header + result.join("\n");
+}
+function generateLocalConfigContent(config) {
+  const tomlObj = localConfigToToml(config);
+  const header = `# search-hub project configuration
+# Project-specific overrides (no secrets - use env vars or global config for API keys)
 
 `;
   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 queriesDir = join(dataDir, "queries");
+async function initLocal(directory, force) {
+  const projectDir = getProjectDir(directory);
+  const configPath = join(projectDir, "config.toml");
+  const sessionsDir = join(projectDir, "sessions");
+  const queriesDir = join(projectDir, "queries");
   const result = {
     success: false,
     configPath,
-    sessionsDir,
-    configDir,
-    dataDir
+    projectDir
   };
-  if (await exists(configDir)) {
+  if (await exists(projectDir)) {
     if (!force) {
       return {
         ...result,
         alreadyExists: true,
-        message: `Configuration directory already exists at ${configDir}. Use --force to overwrite.`
+        message: `Project directory already exists at ${projectDir}. Use --force to overwrite.`
       };
     }
     result.overwritten = true;
   }
-  await mkdir(configDir, { recursive: true });
+  await mkdir(projectDir, { recursive: true });
   await mkdir(sessionsDir, { recursive: true });
   await mkdir(queriesDir, { recursive: true });
   const defaultConfig = getDefaultConfig();
-  defaultConfig.session.directory = sessionsDir;
-  const configContent = generateConfigContent(defaultConfig);
+  const configContent = generateLocalConfigContent(defaultConfig);
   await writeFile(configPath, configContent, "utf-8");
   return {
     ...result,
     success: true,
-    message: result.overwritten ? `Configuration overwritten at ${configDir}` : `Configuration created at ${configDir}`
+    message: result.overwritten ? `Project re-initialized at ${projectDir}` : `Project initialized at ${projectDir}`,
+    hints: [
+      "Set up global credentials: search-hub init --global",
+      "Or use environment variables: see search-hub config --env-vars",
+      "API keys can also be set via .env file in the project root"
+    ]
   };
 }
+async function initGlobal(configDir, force) {
+  const configPath = join(configDir, "config.toml");
+  const result = {
+    success: false,
+    configPath
+  };
+  if (await exists(configDir)) {
+    if (!force) {
+      return {
+        ...result,
+        alreadyExists: true,
+        message: `Global configuration already exists at ${configDir}. Use --force to overwrite.`
+      };
+    }
+    result.overwritten = true;
+  }
+  await mkdir(configDir, { recursive: true });
+  const defaultConfig = getDefaultConfig();
+  const configContent = generateGlobalConfigContent(defaultConfig);
+  await writeFile(configPath, configContent, "utf-8");
+  return {
+    ...result,
+    success: true,
+    message: result.overwritten ? `Global configuration overwritten at ${configDir}` : `Global configuration created at ${configDir}`,
+    hints: [
+      `Edit credentials: search-hub config --global set providers.pubmed.api_key <key>`,
+      `Or edit directly: ${configPath}`
+    ]
+  };
+}
+async function init(options = {}) {
+  const { force = false } = options;
+  if (options.global) {
+    const configDir = options.configDir ?? getConfigDir();
+    return initGlobal(configDir, force);
+  }
+  const directory = options.directory ?? process.cwd();
+  return initLocal(directory, force);
+}
 export {
   init
 };

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

@@ -1 +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  const queriesDir = join(dataDir, 'queries');\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}. 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Override default session directory (empty = platform default)\n\n`;\n\n  const tomlContent = stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n\n  // Add credential hints as comments after provider sections\n  const lines = tomlContent.split('\\n');\n  const result: string[] = [];\n  for (const line of lines) {\n    result.push(line);\n    if (line.startsWith('[providers.pubmed]')) {\n      result.push('# api_key = \"\"    # Optional but recommended (NCBI E-utilities)');\n      result.push('# email = \"\"      # Required by NCBI for tracking');\n    } else if (line.startsWith('[providers.scopus]')) {\n      result.push('# api_key = \"\"    # Required for Scopus access');\n      result.push('# inst_token = \"\" # Optional institutional token');\n    } else if (line.startsWith('[providers.wos]')) {\n      result.push('# api_key = \"\"    # Required for Web of Science');\n    }\n  }\n\n  return header + result.join('\\n');\n}\n\n/**\n * Generate TOML config file content for local project config.\n */\nfunction generateLocalConfigContent(config: Config): string {\n  const tomlObj = localConfigToToml(config);\n  const header = `# search-hub project configuration\n# Project-specific overrides (no secrets - use env vars or global config for API keys)\n\n`;\n  return header + stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n}\n\n/**\n * Initialize a local .search-hub/ project directory.\n */\nasync function initLocal(directory: string, force: boolean): Promise<InitResult> {\n  const projectDir = getProjectDir(directory);\n  const configPath = join(projectDir, 'config.toml');\n  const sessionsDir = join(projectDir, 'sessions');\n  const queriesDir = join(projectDir, 'queries');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\n    projectDir,\n  };\n\n  // Check if .search-hub/ already exists\n  if (await exists(projectDir)) {\n    if (!force) {\n      return {\n        ...result,\n        alreadyExists: true,\n        message: `Project directory already exists at ${projectDir}. Use --force to overwrite.`,\n      };\n    }\n    result.overwritten = true;\n  }\n\n  // Create directories\n  await mkdir(projectDir, { recursive: true });\n  await mkdir(sessionsDir, { recursive: true });\n  await mkdir(queriesDir, { recursive: true });\n\n  // Generate and write local config (no secrets)\n  const defaultConfig = getDefaultConfig();\n  const configContent = generateLocalConfigContent(defaultConfig);\n  await writeFile(configPath, configContent, 'utf-8');\n\n  return {\n    ...result,\n    success: true,\n    message: result.overwritten\n      ? `Project re-initialized at ${projectDir}`\n      : `Project initialized at ${projectDir}`,\n    hints: [\n      'Set up global credentials: search-hub init --global',\n      'Or use environment variables: see search-hub config --env-vars',\n      'API keys can also be set via .env file in the project root',\n    ],\n  };\n}\n\n/**\n * Initialize the global search-hub configuration.\n */\nasync function initGlobal(configDir: string, force: boolean): Promise<InitResult> {\n  const configPath = join(configDir, 'config.toml');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\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: `Global configuration already exists at ${configDir}. 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package/dist/cli/commands/query/init.d.ts

@@ -14,7 +14,6 @@ export declare const QUERY_SCHEMA_FILENAME = "query.schema.json";
  * @returns The YAML template string with comments
  */
 export declare function generateQueryTemplate(title?: string): string;
-export declare const QUERIES_DIR = "queries";
 export interface WriteQueryTemplateOptions {
     title: string;
     output?: string | undefined;

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

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

@@ -1,6 +1,7 @@
 import { access, mkdir, writeFile } from "node:fs/promises";
 import { join, dirname } from "node:path";
 import { generateQueryJSONSchema } from "../../../query/json-schema.js";
+import { getQueriesDir } from "../../../config/paths.js";
 function sanitizeForFilename(title) {
   const result = title.trim().toLowerCase().replace(/\s+/g, "-").replace(/[^a-z0-9_-]/g, "").replace(/-+/g, "-").replace(/^-|-$/g, "");
   if (!result) {
@@ -69,13 +70,12 @@ function generateQueryTemplate(title) {
   const escaped = title.replace(/"/g, '\\"');
   return QUERY_TEMPLATE.replace("name: my_search", `name: "${escaped}"`);
 }
-const QUERIES_DIR = "queries";
 async function writeQueryTemplate(options) {
   const template = generateQueryTemplate(options.title);
   if (options.stdout) {
     return { success: true, message: template };
   }
-  const outputPath = options.output ?? join(options.cwd ?? process.cwd(), QUERIES_DIR, `${sanitizeForFilename(options.title)}.yaml`);
+  const outputPath = options.output ?? join(getQueriesDir(options.cwd), `${sanitizeForFilename(options.title)}.yaml`);
   if (!options.force) {
     try {
       await access(outputPath);
@@ -98,7 +98,6 @@ async function writeQueryTemplate(options) {
   };
 }
 export {
-  QUERIES_DIR,
   QUERY_SCHEMA_FILENAME,
   generateQueryTemplate,
   sanitizeForFilename,

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

@@ -1 +1 @@
-{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access, mkdir } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\nimport { generateQueryJSONSchema } from \"../../../query/json-schema.js\";\n\n/**\n * Sanitize a title string into a safe filename (without extension).\n */\nexport function sanitizeForFilename(title: string): string {\n  const result = title\n    .trim()\n    .toLowerCase()\n    .replace(/\\s+/g, '-')\n    .replace(/[^a-z0-9_-]/g, '')\n    .replace(/-+/g, '-')\n    .replace(/^-|-$/g, '');\n  if (!result) {\n    throw new Error('Title produces an empty filename after sanitization');\n  }\n  return result;\n}\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\nexport const QUERY_SCHEMA_FILENAME = \"query.schema.json\";\n\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  `# yaml-language-server: $schema=./${QUERY_SCHEMA_FILENAME}\\n` +\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - id: concept-1             # Unique block identifier (for provider replacements)\\n\" +\n  \"    field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - id: concept-2\\n\" +\n  \"  #   field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# providers:                 # Optional: per-database block replacements & filter additions\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     replaces:\\n\" +\n  \"#       concept-1:           # Replace block by id\\n\" +\n  \"#         field: keyword\\n\" +\n  \"#         terms:\\n\" +\n  \"#           mesh:\\n\" +\n  \"#             - \\\"MeSH Heading\\\"\\n\" +\n  \"#         operator: OR\\n\" +\n  \"#     adds:\\n\" +\n  \"#       filters:\\n\" +\n  \"#         publication_types:\\n\" +\n  \"#           exclude:\\n\" +\n  \"#             - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @param title - Optional title to set as the query name\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(title?: string): string {\n  if (!title) return QUERY_TEMPLATE;\n  const escaped = title.replace(/\"/g, '\\\\\"');\n  return QUERY_TEMPLATE.replace('name: my_search', `name: \"${escaped}\"`);\n}\n\nexport const QUERIES_DIR = \"queries\";\n\nexport interface WriteQueryTemplateOptions {\n  title: string;\n  output?: string | undefined;\n  stdout?: boolean | undefined;\n  force?: boolean | undefined;\n  cwd?: string | undefined;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * Output priority:\n * 1. --stdout → return template as message (no file)\n * 2. -o <path> → write to that path\n * 3. default → write to queries/<sanitized-title>.yaml\n */\nexport async function writeQueryTemplate(options: WriteQueryTemplateOptions): Promise<{ success: boolean; message: string; outputPath?: string }> {\n  const template = generateQueryTemplate(options.title);\n\n  if (options.stdout) {\n    return { success: true, message: template };\n  }\n\n  // Determine output path\n  const outputPath = options.output\n    ?? join(options.cwd ?? process.cwd(), QUERIES_DIR, `${sanitizeForFilename(options.title)}.yaml`);\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(outputPath);\n      return {\n        success: false,\n        message: `File already exists: ${outputPath}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Ensure parent directory exists\n  await mkdir(dirname(outputPath), { recursive: true });\n\n  // Write template\n  await fsWriteFile(outputPath, template, \"utf-8\");\n\n  // Generate JSON Schema file alongside output\n  const schemaPath = join(dirname(outputPath), QUERY_SCHEMA_FILENAME);\n  const jsonSchema = generateQueryJSONSchema();\n  await fsWriteFile(schemaPath, JSON.stringify(jsonSchema, null, 2) + \"\\n\", \"utf-8\");\n\n  return {\n    success: true,\n    message: `Created: ${outputPath}`,\n    outputPath,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";;;AAYO,SAAS,oBAAoB,OAAuB;AACzD,QAAM,SAAS,MACZ,KAAA,EACA,cACA,QAAQ,QAAQ,GAAG,EACnB,QAAQ,gBAAgB,EAAE,EAC1B,QAAQ,OAAO,GAAG,EAClB,QAAQ,UAAU,EAAE;AACvB,MAAI,CAAC,QAAQ;AACX,UAAM,IAAI,MAAM,qDAAqD;AAAA,EACvE;AACA,SAAO;AACT;AAMO,MAAM,wBAAwB;AAGrC,MAAM,iBACJ,qCAAqC,qBAAqB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA6DrD,SAAS,sBAAsB,OAAwB;AAC5D,MAAI,CAAC,MAAO,QAAO;AACnB,QAAM,UAAU,MAAM,QAAQ,MAAM,KAAK;AACzC,SAAO,eAAe,QAAQ,mBAAmB,UAAU,OAAO,GAAG;AACvE;AAEO,MAAM,cAAc;AAkB3B,eAAsB,mBAAmB,SAAyG;AAChJ,QAAM,WAAW,sBAAsB,QAAQ,KAAK;AAEpD,MAAI,QAAQ,QAAQ;AAClB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,QAAM,aAAa,QAAQ,UACtB,KAAK,QAAQ,OAAO,QAAQ,IAAA,GAAO,aAAa,GAAG,oBAAoB,QAAQ,KAAK,CAAC,OAAO;AAGjG,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,UAAU;AACvB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,UAAU;AAAA,MAAA;AAAA,IAE/C,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAM,MAAM,QAAQ,UAAU,GAAG,EAAE,WAAW,MAAM;AAGpD,QAAMA,UAAY,YAAY,UAAU,OAAO;AAG/C,QAAM,aAAa,KAAK,QAAQ,UAAU,GAAG,qBAAqB;AAClE,QAAM,aAAa,wBAAA;AACnB,QAAMA,UAAY,YAAY,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEjF,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,YAAY,UAAU;AAAA,IAC/B;AAAA,EAAA;AAEJ;"}
+{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access, mkdir } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\nimport { generateQueryJSONSchema } from \"../../../query/json-schema.js\";\nimport { getQueriesDir } from \"../../../config/paths.js\";\n\n/**\n * Sanitize a title string into a safe filename (without extension).\n */\nexport function sanitizeForFilename(title: string): string {\n  const result = title\n    .trim()\n    .toLowerCase()\n    .replace(/\\s+/g, '-')\n    .replace(/[^a-z0-9_-]/g, '')\n    .replace(/-+/g, '-')\n    .replace(/^-|-$/g, '');\n  if (!result) {\n    throw new Error('Title produces an empty filename after sanitization');\n  }\n  return result;\n}\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\nexport const QUERY_SCHEMA_FILENAME = \"query.schema.json\";\n\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  `# yaml-language-server: $schema=./${QUERY_SCHEMA_FILENAME}\\n` +\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - id: concept-1             # Unique block identifier (for provider replacements)\\n\" +\n  \"    field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - id: concept-2\\n\" +\n  \"  #   field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# providers:                 # Optional: per-database block replacements & filter additions\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     replaces:\\n\" +\n  \"#       concept-1:           # Replace block by id\\n\" +\n  \"#         field: keyword\\n\" +\n  \"#         terms:\\n\" +\n  \"#           mesh:\\n\" +\n  \"#             - \\\"MeSH Heading\\\"\\n\" +\n  \"#         operator: OR\\n\" +\n  \"#     adds:\\n\" +\n  \"#       filters:\\n\" +\n  \"#         publication_types:\\n\" +\n  \"#           exclude:\\n\" +\n  \"#             - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @param title - Optional title to set as the query name\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(title?: string): string {\n  if (!title) return QUERY_TEMPLATE;\n  const escaped = title.replace(/\"/g, '\\\\\"');\n  return QUERY_TEMPLATE.replace('name: my_search', `name: \"${escaped}\"`);\n}\n\n\nexport interface WriteQueryTemplateOptions {\n  title: string;\n  output?: string | undefined;\n  stdout?: boolean | undefined;\n  force?: boolean | undefined;\n  cwd?: string | undefined;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * Output priority:\n * 1. --stdout → return template as message (no file)\n * 2. -o <path> → write to that path\n * 3. default → write to queries/<sanitized-title>.yaml\n */\nexport async function writeQueryTemplate(options: WriteQueryTemplateOptions): Promise<{ success: boolean; message: string; outputPath?: string }> {\n  const template = generateQueryTemplate(options.title);\n\n  if (options.stdout) {\n    return { success: true, message: template };\n  }\n\n  // Determine output path\n  const outputPath = options.output\n    ?? join(getQueriesDir(options.cwd), `${sanitizeForFilename(options.title)}.yaml`);\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(outputPath);\n      return {\n        success: false,\n        message: `File already exists: ${outputPath}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Ensure parent directory exists\n  await mkdir(dirname(outputPath), { recursive: true });\n\n  // Write template\n  await fsWriteFile(outputPath, template, \"utf-8\");\n\n  // Generate JSON Schema file alongside output\n  const schemaPath = join(dirname(outputPath), QUERY_SCHEMA_FILENAME);\n  const jsonSchema = generateQueryJSONSchema();\n  await fsWriteFile(schemaPath, JSON.stringify(jsonSchema, null, 2) + \"\\n\", \"utf-8\");\n\n  return {\n    success: true,\n    message: `Created: ${outputPath}`,\n    outputPath,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";;;;AAaO,SAAS,oBAAoB,OAAuB;AACzD,QAAM,SAAS,MACZ,KAAA,EACA,cACA,QAAQ,QAAQ,GAAG,EACnB,QAAQ,gBAAgB,EAAE,EAC1B,QAAQ,OAAO,GAAG,EAClB,QAAQ,UAAU,EAAE;AACvB,MAAI,CAAC,QAAQ;AACX,UAAM,IAAI,MAAM,qDAAqD;AAAA,EACvE;AACA,SAAO;AACT;AAMO,MAAM,wBAAwB;AAGrC,MAAM,iBACJ,qCAAqC,qBAAqB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA6DrD,SAAS,sBAAsB,OAAwB;AAC5D,MAAI,CAAC,MAAO,QAAO;AACnB,QAAM,UAAU,MAAM,QAAQ,MAAM,KAAK;AACzC,SAAO,eAAe,QAAQ,mBAAmB,UAAU,OAAO,GAAG;AACvE;AAmBA,eAAsB,mBAAmB,SAAyG;AAChJ,QAAM,WAAW,sBAAsB,QAAQ,KAAK;AAEpD,MAAI,QAAQ,QAAQ;AAClB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,QAAM,aAAa,QAAQ,UACtB,KAAK,cAAc,QAAQ,GAAG,GAAG,GAAG,oBAAoB,QAAQ,KAAK,CAAC,OAAO;AAGlF,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,UAAU;AACvB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,UAAU;AAAA,MAAA;AAAA,IAE/C,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAM,MAAM,QAAQ,UAAU,GAAG,EAAE,WAAW,MAAM;AAGpD,QAAMA,UAAY,YAAY,UAAU,OAAO;AAG/C,QAAM,aAAa,KAAK,QAAQ,UAAU,GAAG,qBAAqB;AAClE,QAAM,aAAa,wBAAA;AACnB,QAAMA,UAAY,YAAY,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEjF,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,YAAY,UAAU;AAAA,IAC/B;AAAA,EAAA;AAEJ;"}

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

@@ -1 +1 @@
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+{"version":3,"file":"resolve.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/resolve.ts"],"names":[],"mappings":"AAcA,qBAAa,aAAc,SAAQ,KAAK;gBAC1B,IAAI,EAAE,MAAM;CAIzB;AAiBD,wBAAsB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CA2CnE"}

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

@@ -1,4 +1,6 @@
 import { stat } from "node:fs/promises";
+import { relative } from "node:path";
+import { getQueriesDir } from "../../../config/paths.js";
 class NotAFileError extends Error {
   constructor(path) {
     super(`Path is not a file: ${path}`);
@@ -31,14 +33,15 @@ async function resolveQueryFile(arg) {
       return withExt;
     }
   }
+  const queriesDir = relative(process.cwd(), getQueriesDir());
   const basename = arg.endsWith(".yaml") || arg.endsWith(".yml") ? arg : `${arg}.yaml`;
-  const inQueries = `queries/${basename}`;
+  const inQueries = `${queriesDir}/${basename}`;
   candidates.push(inQueries);
   if (await isFile(inQueries)) {
     return inQueries;
   }
   if (!arg.endsWith(".yaml") && !arg.endsWith(".yml")) {
-    const inQueriesYml = `queries/${arg}.yml`;
+    const inQueriesYml = `${queriesDir}/${arg}.yml`;
     candidates.push(inQueriesYml);
     if (await isFile(inQueriesYml)) {
       return inQueriesYml;

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

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

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