@ncukondo/search-hub 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2024 ncukondo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @ncukondo/search-hub
+
+[![npm version](https://img.shields.io/npm/v/@ncukondo/search-hub.svg)](https://www.npmjs.com/package/@ncukondo/search-hub)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+A CLI tool for systematic literature searching across multiple academic databases.
+
+## Features
+
+- **Multi-database search**: PubMed, ERIC, arXiv, Scopus (Web of Science, Embase planned)
+- **Unified query syntax**: YAML-based DSL with automatic translation
+- **Reproducible searches**: Full session logging for PRISMA reporting
+- **Resume support**: Continue interrupted searches at DB or page level
+- **Reference manager integration**: Works with [reference-manager](https://github.com/ncukondo/reference-manager)
+
+## Installation
+
+```bash
+npm install -g @ncukondo/search-hub
+```
+
+Requires Node.js 22+.
+
+## Quick Start
+
+1. Initialize configuration:
+```bash
+search-hub init
+```
+
+This creates config and data directories in platform-specific locations:
+
+| Platform | Config | Data |
+|----------|--------|------|
+| Linux | `~/.config/search-hub/` | `~/.local/share/search-hub/` |
+| macOS | `~/Library/Preferences/search-hub/` | `~/Library/Application Support/search-hub/` |
+| Windows | `%APPDATA%/search-hub/Config/` | `%LOCALAPPDATA%/search-hub/Data/` |
+
+2. Create a query file (`query.yaml`):
+```yaml
+name: my_review
+description: "Literature search for scoping review"
+
+query:
+  - field: title_abstract
+    terms:
+      keywords:
+        - diabetes
+        - "machine learning"
+    operator: OR
+
+filters:
+  year_from: 2020
+  language:
+    - en
+```
+
+3. Run search:
+```bash
+search-hub search query.yaml
+```
+
+4. Export results:
+```bash
+search-hub export <session-id> --format ids
+```
+
+## Documentation
+
+- [Query Guide](./docs/query-guide.md) - How to write query files
+- [Command Reference](./docs/commands.md) - All CLI commands and options
+- [Configuration](./docs/configuration.md) - Setup and configuration
+- [Databases](./docs/databases.md) - Supported databases and tips
+
+## Development
+
+```bash
+# Install dependencies
+npm install
+
+# Run tests
+npm test
+
+# Lint
+npm run lint
+
+# Build
+npm run build
+```
+
+## License
+
+MIT

package/dist/_virtual/___vite-browser-external.js

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+import * as __viteBrowserExternal from "./__vite-browser-external.js";
+import { getAugmentedNamespace } from "./_commonjsHelpers.js";
+const require$$3 = /* @__PURE__ */ getAugmentedNamespace(__viteBrowserExternal);
+export {
+  require$$3 as default
+};
+//# sourceMappingURL=___vite-browser-external.js.map

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package/dist/_virtual/__vite-browser-external.js

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+export {
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+};
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package/dist/_virtual/_commonjsHelpers.js

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+function getAugmentedNamespace(n) {
+  if (Object.prototype.hasOwnProperty.call(n, "__esModule")) return n;
+  var f = n.default;
+  if (typeof f == "function") {
+    var a = function a2() {
+      if (this instanceof a2) {
+        return Reflect.construct(f, arguments, this.constructor);
+      }
+      return f.apply(this, arguments);
+    };
+    a.prototype = f.prototype;
+  } else a = {};
+  Object.defineProperty(a, "__esModule", { value: true });
+  Object.keys(n).forEach(function(k) {
+    var d = Object.getOwnPropertyDescriptor(n, k);
+    Object.defineProperty(a, k, d.get ? d : {
+      enumerable: true,
+      get: function() {
+        return n[k];
+      }
+    });
+  });
+  return a;
+}
+export {
+  getAugmentedNamespace
+};
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package/dist/_virtual/cli-progress.js

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+import { __require as requireCliProgress } from "../node_modules/cli-progress/cli-progress.js";
+var cliProgressExports = requireCliProgress();
+export {
+  cliProgressExports as c
+};
+//# sourceMappingURL=cli-progress.js.map

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package/dist/_virtual/index.js

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+var stringWidth = { exports: {} };
+export {
+  stringWidth as __module
+};
+//# sourceMappingURL=index.js.map

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package/dist/_virtual/index2.js

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+export {
+  isFullwidthCodePoint as __module
+};
+//# sourceMappingURL=index2.js.map

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

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+import { Config } from '../../config/index.js';
+/**
+ * Result of a config operation.
+ */
+export interface ConfigResult {
+    success: boolean;
+    value?: string;
+    error?: string;
+}
+/**
+ * Get a nested value from an object using dot notation.
+ *
+ * @example
+ * getNestedValue({ a: { b: 1 } }, 'a.b') // returns 1
+ */
+export declare function getNestedValue(obj: Record<string, unknown>, path: string): unknown;
+/**
+ * Set a nested value in an object using dot notation.
+ *
+ * @example
+ * setNestedValue({ a: { b: 1 } }, 'a.b', 2) // modifies obj to { a: { b: 2 } }
+ */
+export declare function setNestedValue(obj: Record<string, unknown>, path: string, value: unknown): void;
+/**
+ * View all configuration values.
+ */
+export declare function viewConfig(config: Config): string;
+/**
+ * View a specific configuration key.
+ */
+export declare function viewConfigKey(config: Config, key: string): ConfigResult;
+/**
+ * Set a configuration key to a new value.
+ * Only allows setting keys that already exist in the configuration.
+ */
+export declare function setConfigKey(config: Config, key: string, value: string): ConfigResult;
+//# sourceMappingURL=config.d.ts.map

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package/dist/cli/commands/config.js

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+function getNestedValue(obj, path) {
+  const keys = path.split(".");
+  let current = obj;
+  for (const key of keys) {
+    if (current === null || current === void 0) {
+      return void 0;
+    }
+    if (typeof current !== "object") {
+      return void 0;
+    }
+    current = current[key];
+  }
+  return current;
+}
+function setNestedValue(obj, path, value) {
+  const keys = path.split(".");
+  let current = obj;
+  for (let i = 0; i < keys.length - 1; i++) {
+    const key = keys[i];
+    if (!(key in current) || typeof current[key] !== "object") {
+      current[key] = {};
+    }
+    current = current[key];
+  }
+  const lastKey = keys[keys.length - 1];
+  current[lastKey] = value;
+}
+function flattenObject(obj, prefix = "") {
+  const result = [];
+  for (const [key, value] of Object.entries(obj)) {
+    const fullKey = prefix ? `${prefix}.${key}` : key;
+    if (value !== null && typeof value === "object" && !Array.isArray(value)) {
+      result.push(
+        ...flattenObject(value, fullKey)
+      );
+    } else {
+      result.push({ key: fullKey, value });
+    }
+  }
+  return result;
+}
+function formatValue(value) {
+  if (value === null) return "null";
+  if (value === void 0) return "undefined";
+  if (typeof value === "string") return value;
+  if (typeof value === "object") return JSON.stringify(value, null, 2);
+  return String(value);
+}
+function viewConfig(config) {
+  const flattened = flattenObject(config);
+  const lines = flattened.map(({ key, value }) => {
+    const formattedValue = formatValue(value);
+    return `${key} = ${formattedValue}`;
+  });
+  return lines.join("\n");
+}
+function viewConfigKey(config, key) {
+  const value = getNestedValue(
+    config,
+    key
+  );
+  if (value === void 0) {
+    return {
+      success: false,
+      error: `Key "${key}" not found in configuration`
+    };
+  }
+  return {
+    success: true,
+    value: formatValue(value)
+  };
+}
+function parseValue(value, existingValue) {
+  if (value === "true") return true;
+  if (value === "false") return false;
+  if (typeof existingValue === "number") {
+    const num = Number(value);
+    if (!isNaN(num)) return num;
+  }
+  return value;
+}
+function setConfigKey(config, key, value) {
+  if (!key) {
+    return {
+      success: false,
+      error: "Key cannot be empty"
+    };
+  }
+  const existingValue = getNestedValue(
+    config,
+    key
+  );
+  if (existingValue === void 0) {
+    return {
+      success: false,
+      error: `Unknown configuration key: "${key}". Use "search-hub config" to see available keys.`
+    };
+  }
+  const parsedValue = parseValue(value, existingValue);
+  setNestedValue(
+    config,
+    key,
+    parsedValue
+  );
+  return {
+    success: true,
+    value: formatValue(parsedValue)
+  };
+}
+export {
+  getNestedValue,
+  setConfigKey,
+  setNestedValue,
+  viewConfig,
+  viewConfigKey
+};
+//# sourceMappingURL=config.js.map

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

@@ -0,0 +1,26 @@
+import { ProviderName, Article } from '../../providers/base/types.js';
+export type ExportFormat = 'ids' | 'json' | 'jsonl';
+export type IdType = 'doi' | 'pmid' | 'all';
+export interface ExportCommandOptions {
+    sessionId: string;
+    format: ExportFormat;
+    outputPath?: string;
+    providers?: ProviderName[];
+    idType?: IdType;
+}
+export interface CommandLineOptions {
+    format?: string | undefined;
+    output?: string | undefined;
+    db?: string | undefined;
+    idType?: string | undefined;
+}
+export interface ValidationResult {
+    valid: boolean;
+    error?: string;
+}
+export declare function parseExportOptions(sessionId: string, options: CommandLineOptions): ExportCommandOptions;
+export declare function validateExportInput(options: ExportCommandOptions): ValidationResult;
+export declare function formatIds(articles: Article[], idType: IdType): string;
+export declare function formatJson(articles: Article[]): string;
+export declare function formatJsonl(articles: Article[]): string;
+//# sourceMappingURL=export.d.ts.map

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

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package/dist/cli/commands/export.js

@@ -0,0 +1,86 @@
+import { parseProviderNames } from "../utils/validation.js";
+const VALID_FORMATS = ["ids", "json", "jsonl"];
+const VALID_ID_TYPES = ["doi", "pmid", "all"];
+function parseExportOptions(sessionId, options) {
+  const result = {
+    sessionId,
+    format: options.format || "jsonl"
+  };
+  if (options.output) {
+    result.outputPath = options.output;
+  }
+  if (options.db) {
+    result.providers = parseProviderNames(options.db);
+  }
+  if (options.idType) {
+    result.idType = options.idType;
+  }
+  return result;
+}
+function validateExportInput(options) {
+  if (!options.sessionId || options.sessionId.trim() === "") {
+    return {
+      valid: false,
+      error: "A session ID is required"
+    };
+  }
+  if (!VALID_FORMATS.includes(options.format)) {
+    return {
+      valid: false,
+      error: `Invalid format: ${options.format}. Valid formats are: ${VALID_FORMATS.join(", ")}`
+    };
+  }
+  if (options.idType) {
+    if (!VALID_ID_TYPES.includes(options.idType)) {
+      return {
+        valid: false,
+        error: `Invalid id-type: ${options.idType}. Valid types are: ${VALID_ID_TYPES.join(", ")}`
+      };
+    }
+    if (options.format !== "ids") {
+      return {
+        valid: false,
+        error: "--id-type can only be used with --format ids"
+      };
+    }
+  }
+  return { valid: true };
+}
+function formatIds(articles, idType) {
+  const ids = [];
+  for (const article of articles) {
+    if (idType === "doi") {
+      if (article.doi) {
+        ids.push(article.doi);
+      }
+    } else if (idType === "pmid") {
+      if (article.pmid) {
+        ids.push(article.pmid);
+      }
+    } else if (idType === "all") {
+      if (article.doi) ids.push(`doi:${article.doi}`);
+      if (article.pmid) ids.push(`pmid:${article.pmid}`);
+      if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);
+      if (article.scopusId) ids.push(`scopus:${article.scopusId}`);
+      if (article.ericId) ids.push(`eric:${article.ericId}`);
+    }
+  }
+  return ids.join("\n");
+}
+function formatJson(articles) {
+  return JSON.stringify(articles, null, 2);
+}
+function formatJsonl(articles) {
+  if (articles.length === 0) {
+    return "";
+  }
+  return articles.map((article) => JSON.stringify(article)).join("\n");
+}
+export {
+  formatIds,
+  formatJson,
+  formatJsonl,
+  parseExportOptions,
+  validateExportInput
+};
+//# sourceMappingURL=export.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"export.js","sources":["../../../src/cli/commands/export.ts"],"sourcesContent":["import type { ProviderName } from '../../providers/base/types.js';\nimport type { Article } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\n\nexport type ExportFormat = 'ids' | 'json' | 'jsonl';\nexport type IdType = 'doi' | 'pmid' | 'all';\n\nexport interface ExportCommandOptions {\n  sessionId: string;\n  format: ExportFormat;\n  outputPath?: string;\n  providers?: ProviderName[];\n  idType?: IdType;\n}\n\nexport interface CommandLineOptions {\n  format?: string | undefined;\n  output?: string | undefined;\n  db?: string | undefined;\n  idType?: string | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nconst VALID_FORMATS: ExportFormat[] = ['ids', 'json', 'jsonl'];\nconst VALID_ID_TYPES: IdType[] = ['doi', 'pmid', 'all'];\n\nexport function parseExportOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ExportCommandOptions {\n  const result: ExportCommandOptions = {\n    sessionId,\n    format: (options.format as ExportFormat) || 'jsonl',\n  };\n\n  if (options.output) {\n    result.outputPath = options.output;\n  }\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.idType) {\n    result.idType = options.idType as IdType;\n  }\n\n  return result;\n}\n\nexport function validateExportInput(options: ExportCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  if (!VALID_FORMATS.includes(options.format)) {\n    return {\n      valid: false,\n      error: `Invalid format: ${options.format}. Valid formats are: ${VALID_FORMATS.join(', ')}`,\n    };\n  }\n\n  if (options.idType) {\n    if (!VALID_ID_TYPES.includes(options.idType)) {\n      return {\n        valid: false,\n        error: `Invalid id-type: ${options.idType}. 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package/dist/cli/commands/init.d.ts

@@ -0,0 +1,45 @@
+/**
+ * Options for the init command.
+ */
+export interface InitOptions {
+    /** Config directory (defaults to platform-specific via getConfigDir()) */
+    configDir?: string;
+    /** Data directory (defaults to platform-specific via getDataDir()) */
+    dataDir?: string;
+    /** Force overwrite if directory already exists */
+    force?: boolean;
+}
+/**
+ * Result of the init command.
+ */
+export interface InitResult {
+    /** Whether initialization was successful */
+    success: boolean;
+    /** Path to the created config file */
+    configPath: string;
+    /** Path to the sessions directory */
+    sessionsDir: string;
+    /** Path to the config directory */
+    configDir: string;
+    /** Path to the data directory */
+    dataDir: string;
+    /** Whether files already existed (only when success=false) */
+    alreadyExists?: boolean;
+    /** Whether existing files were overwritten (only when force=true) */
+    overwritten?: boolean;
+    /** Message describing the result */
+    message?: string;
+}
+/**
+ * Initialize the search-hub configuration directory.
+ *
+ * Creates:
+ * - Config directory with config.toml
+ * - Data directory with sessions/ subdirectory
+ *
+ * On Linux (XDG):
+ * - ~/.config/search-hub/config.toml
+ * - ~/.local/share/search-hub/sessions/
+ */
+export declare function init(options?: InitOptions): Promise<InitResult>;
+//# sourceMappingURL=init.d.ts.map

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

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