@ncukondo/search-hub 0.20.1 → 0.22.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +44 -22
- package/dist/cli/commands/init.d.ts.map +1 -1
- package/dist/cli/commands/init.js +2 -0
- package/dist/cli/commands/init.js.map +1 -1
- package/dist/cli/commands/query/init.d.ts +20 -9
- package/dist/cli/commands/query/init.d.ts.map +1 -1
- package/dist/cli/commands/query/init.js +25 -10
- package/dist/cli/commands/query/init.js.map +1 -1
- package/dist/cli/commands/query/resolve.d.ts +5 -0
- package/dist/cli/commands/query/resolve.d.ts.map +1 -0
- package/dist/cli/commands/query/resolve.js +59 -0
- package/dist/cli/commands/query/resolve.js.map +1 -0
- package/dist/cli/entry-bun.d.ts +2 -0
- package/dist/cli/entry-bun.d.ts.map +1 -0
- package/dist/cli/index.d.ts.map +1 -1
- package/dist/cli/index.js +58 -30
- package/dist/cli/index.js.map +1 -1
- package/dist/cli/suggestions/rules.d.ts.map +1 -1
- package/dist/cli/suggestions/rules.js +21 -9
- package/dist/cli/suggestions/rules.js.map +1 -1
- package/dist/cli/suggestions/types.d.ts +2 -0
- package/dist/cli/suggestions/types.d.ts.map +1 -1
- package/dist/node_modules/dom-serializer/lib/index.js +1 -1
- package/dist/node_modules/domelementtype/lib/index.js +1 -1
- package/dist/node_modules/nth-check/lib/index.js +1 -1
- package/dist/package.json.js +9 -0
- package/dist/package.json.js.map +1 -0
- package/dist/version.d.ts.map +1 -1
- package/dist/version.js +1 -3
- package/dist/version.js.map +1 -1
- package/package.json +1 -1
package/README.md
CHANGED
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@@ -21,6 +21,26 @@ A CLI tool for systematic literature searching across multiple academic database
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## Installation
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### Binary (no Node.js required)
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Download the latest binary for your platform:
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**Linux / macOS (Intel & Apple Silicon):**
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```bash
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curl -fsSL https://raw.githubusercontent.com/ncukondo/search-hub/main/install.sh | bash
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```
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**Windows (PowerShell):**
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```powershell
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irm https://raw.githubusercontent.com/ncukondo/search-hub/main/install.ps1 | iex
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```
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Or download manually from [GitHub Releases](https://github.com/ncukondo/search-hub/releases).
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### npm
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```bash
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npm install -g @ncukondo/search-hub
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```
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@@ -44,14 +64,14 @@ This creates config and data directories in platform-specific locations:
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2. Create a query file:
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```bash
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search-hub query init
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search-hub query init "my review"
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```
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This
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This creates `queries/my-review.yaml` with JSON Schema support for editor autocompletion. Edit it to define your search:
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```yaml
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# yaml-language-server: $schema=./query.schema.json
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name:
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name: "my review"
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description: "Literature search for scoping review"
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query:
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3. Validate the query:
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```bash
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search-hub query validate
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search-hub query validate my-review
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```
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This checks structure, validates controlled vocabulary terms (MeSH, ERIC descriptors, Emtree) against external APIs, and suggests corrections for typos.
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This checks structure, validates controlled vocabulary terms (MeSH, ERIC descriptors, Emtree) against external APIs, and suggests corrections for typos. The query name is automatically resolved to `queries/my-review.yaml`.
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4. Run search:
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```bash
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search-hub search
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search-hub search my-review
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```
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5. Export results:
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### Workflow
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1. **
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1. **Create a query** - Start with a template:
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```bash
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search-hub
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search-hub query init "my review"
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# Creates queries/my-review.yaml
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```
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2. **
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2. **Check hit counts** - Preview before downloading:
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```bash
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search-hub
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search-hub results <session-v1> -q "title:diabetes year:2023-2025"
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search-hub search my-review --count-only
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```
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3. **
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3. **Run the search** - When counts look good:
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```bash
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search-hub
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search-hub search my-review
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```
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4. **
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4. **Review results** - Check titles to assess quality:
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```bash
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search-hub results <session-id> --limit 50
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search-hub results <session-id> -q "title:diabetes year:2023-2025"
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```
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5. **
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5. **Refine and re-run** - Edit the query file, then iterate:
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```bash
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$EDITOR queries/my-review.yaml
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search-hub search my-review --count-only # Re-check counts
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search-hub search my-review # Execute full search
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```
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6. **Compare results with diff** - See what changed:
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- **Use `--count-only` first**: Check hit counts before downloading full results.
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```bash
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search-hub search
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search-hub search my-review --count-only
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```
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- **Use `--preview`** to see hit counts with sample titles:
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```bash
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search-hub search
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search-hub search my-review --preview
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```
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- **Use `--dry-run`** to preview translations: See exactly what query each database will receive.
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```bash
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search-hub search
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search-hub search my-review --dry-run
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```
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- **Compare removed articles carefully**: When narrowing a search, `--show removed` reveals what you're excluding. If important papers are removed, your refinement may be too aggressive.
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- **
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- **Track iterations**: Use `query assess` and `query log` to record and review your refinement history.
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## Fulltext Retrieval
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{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/init.ts"],"names":[],"mappings":"AAOA;;GAEG;AACH,MAAM,WAAW,WAAW;IAC1B,0EAA0E;IAC1E,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,sEAAsE;IACtE,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,kDAAkD;IAClD,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,4CAA4C;IAC5C,OAAO,EAAE,OAAO,CAAC;IACjB,sCAAsC;IACtC,UAAU,EAAE,MAAM,CAAC;IACnB,qCAAqC;IACrC,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iCAAiC;IACjC,OAAO,EAAE,MAAM,CAAC;IAChB,8DAA8D;IAC9D,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,qEAAqE;IACrE,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,oCAAoC;IACpC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAqGD;;;;;;;;;;GAUG;AACH,wBAAsB,IAAI,CAAC,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,UAAU,CAAC,
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{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/init.ts"],"names":[],"mappings":"AAOA;;GAEG;AACH,MAAM,WAAW,WAAW;IAC1B,0EAA0E;IAC1E,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,sEAAsE;IACtE,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,kDAAkD;IAClD,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,4CAA4C;IAC5C,OAAO,EAAE,OAAO,CAAC;IACjB,sCAAsC;IACtC,UAAU,EAAE,MAAM,CAAC;IACnB,qCAAqC;IACrC,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iCAAiC;IACjC,OAAO,EAAE,MAAM,CAAC;IAChB,8DAA8D;IAC9D,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,qEAAqE;IACrE,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,oCAAoC;IACpC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAqGD;;;;;;;;;;GAUG;AACH,wBAAsB,IAAI,CAAC,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,UAAU,CAAC,CAmDzE"}
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} = options;
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const configPath = join(configDir, "config.toml");
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const sessionsDir = join(dataDir, "sessions");
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const queriesDir = join(dataDir, "queries");
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const result = {
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success: false,
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}
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await mkdir(configDir, { recursive: true });
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await mkdir(sessionsDir, { recursive: true });
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await mkdir(queriesDir, { recursive: true });
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const defaultConfig = getDefaultConfig();
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defaultConfig.session.directory = sessionsDir;
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const configContent = generateConfigContent(defaultConfig);
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{"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}. 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{"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 ${configDir}. 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{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/init.ts"],"names":[],"mappings":"AASA;;;GAGG;AACH,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AA2DzD
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{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/init.ts"],"names":[],"mappings":"AASA;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAYzD;AAED;;;GAGG;AACH,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AA2DzD;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,MAAM,CAI5D;AAED,eAAO,MAAM,WAAW,YAAY,CAAC;AAErC,MAAM,WAAW,yBAAyB;IACxC,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC5B,MAAM,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC7B,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC1B;AAED;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CAAC,OAAO,EAAE,yBAAyB,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAwChJ"}
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name: my_search
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@@ -57,36 +64,44 @@ query:
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# exclude:
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# - "Letter"
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`;
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function generateQueryTemplate() {
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return QUERY_TEMPLATE;
|
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function generateQueryTemplate(title) {
|
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if (!title) return QUERY_TEMPLATE;
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const escaped = title.replace(/"/g, '\\"');
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return QUERY_TEMPLATE.replace("name: my_search", `name: "${escaped}"`);
|
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const QUERIES_DIR = "queries";
|
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async function writeQueryTemplate(options) {
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const template = generateQueryTemplate();
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if (
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const template = generateQueryTemplate(options.title);
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if (options.stdout) {
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const outputPath = options.output ?? join(options.cwd ?? process.cwd(), QUERIES_DIR, `${sanitizeForFilename(options.title)}.yaml`);
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try {
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await access(
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await access(outputPath);
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success: false,
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message: `File already exists: ${
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message: `File already exists: ${outputPath}. Use --force to overwrite.`
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};
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} catch {
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}
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}
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await
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await mkdir(dirname(outputPath), { recursive: true });
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await writeFile(outputPath, template, "utf-8");
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export {
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generateQueryTemplate,
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writeQueryTemplate
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};
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//# sourceMappingURL=init.js.map
|
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@@ -1 +1 @@
|
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-
{"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 } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\nimport { generateQueryJSONSchema } from \"../../../query/json-schema.js\";\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 * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n *
|
|
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;"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"resolve.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/query/resolve.ts"],"names":[],"mappings":"AAYA,qBAAa,aAAc,SAAQ,KAAK;gBAC1B,IAAI,EAAE,MAAM;CAIzB;AAiBD,wBAAsB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CA0CnE"}
|
|
@@ -0,0 +1,59 @@
|
|
|
1
|
+
import { stat } from "node:fs/promises";
|
|
2
|
+
class NotAFileError extends Error {
|
|
3
|
+
constructor(path) {
|
|
4
|
+
super(`Path is not a file: ${path}`);
|
|
5
|
+
this.name = "NotAFileError";
|
|
6
|
+
}
|
|
7
|
+
}
|
|
8
|
+
async function isFile(path) {
|
|
9
|
+
try {
|
|
10
|
+
const s = await stat(path);
|
|
11
|
+
if (!s.isFile()) {
|
|
12
|
+
throw new NotAFileError(path);
|
|
13
|
+
}
|
|
14
|
+
return true;
|
|
15
|
+
} catch (error) {
|
|
16
|
+
if (error instanceof NotAFileError) {
|
|
17
|
+
throw error;
|
|
18
|
+
}
|
|
19
|
+
return false;
|
|
20
|
+
}
|
|
21
|
+
}
|
|
22
|
+
async function resolveQueryFile(arg) {
|
|
23
|
+
if (await isFile(arg)) {
|
|
24
|
+
return arg;
|
|
25
|
+
}
|
|
26
|
+
const candidates = [];
|
|
27
|
+
if (!arg.endsWith(".yaml") && !arg.endsWith(".yml")) {
|
|
28
|
+
const withExt = `${arg}.yaml`;
|
|
29
|
+
candidates.push(withExt);
|
|
30
|
+
if (await isFile(withExt)) {
|
|
31
|
+
return withExt;
|
|
32
|
+
}
|
|
33
|
+
}
|
|
34
|
+
const basename = arg.endsWith(".yaml") || arg.endsWith(".yml") ? arg : `${arg}.yaml`;
|
|
35
|
+
const inQueries = `queries/${basename}`;
|
|
36
|
+
candidates.push(inQueries);
|
|
37
|
+
if (await isFile(inQueries)) {
|
|
38
|
+
return inQueries;
|
|
39
|
+
}
|
|
40
|
+
if (!arg.endsWith(".yaml") && !arg.endsWith(".yml")) {
|
|
41
|
+
const inQueriesYml = `queries/${arg}.yml`;
|
|
42
|
+
candidates.push(inQueriesYml);
|
|
43
|
+
if (await isFile(inQueriesYml)) {
|
|
44
|
+
return inQueriesYml;
|
|
45
|
+
}
|
|
46
|
+
}
|
|
47
|
+
const tried = [`./${arg}`, ...candidates.map((c) => `./${c}`)];
|
|
48
|
+
throw new Error(
|
|
49
|
+
`Query file not found: "${arg}"
|
|
50
|
+
Tried:
|
|
51
|
+
` + tried.map((p) => ` ${p}`).join("\n") + `
|
|
52
|
+
Create a new query: search-hub query init "${arg}"`
|
|
53
|
+
);
|
|
54
|
+
}
|
|
55
|
+
export {
|
|
56
|
+
NotAFileError,
|
|
57
|
+
resolveQueryFile
|
|
58
|
+
};
|
|
59
|
+
//# sourceMappingURL=resolve.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"resolve.js","sources":["../../../../src/cli/commands/query/resolve.ts"],"sourcesContent":["/**\n * Smart query file resolution.\n *\n * Resolution order:\n * 1. Exact path exists → use it\n * 2. <arg>.yaml exists → use it\n * 3. queries/<arg>.yaml exists → use it\n * 4. queries/<arg>.yml exists → use it\n * 5. Error with tried paths\n */\nimport { stat } from 'node:fs/promises';\n\nexport class NotAFileError extends Error {\n constructor(path: string) {\n super(`Path is not a file: ${path}`);\n this.name = 'NotAFileError';\n }\n}\n\nasync function isFile(path: string): Promise<boolean> {\n try {\n const s = await stat(path);\n if (!s.isFile()) {\n throw new NotAFileError(path);\n }\n return true;\n } catch (error) {\n if (error instanceof NotAFileError) {\n throw error;\n }\n return false;\n }\n}\n\nexport async function resolveQueryFile(arg: string): Promise<string> {\n // 1. Exact path\n if (await isFile(arg)) {\n return arg;\n }\n\n const candidates: string[] = [];\n\n // 2. arg + .yaml (skip if already ends with .yaml)\n if (!arg.endsWith('.yaml') && !arg.endsWith('.yml')) {\n const withExt = `${arg}.yaml`;\n candidates.push(withExt);\n if (await isFile(withExt)) {\n return withExt;\n }\n }\n\n // 3. queries/<arg>.yaml\n const basename = arg.endsWith('.yaml') || arg.endsWith('.yml') ? arg : `${arg}.yaml`;\n const inQueries = `queries/${basename}`;\n candidates.push(inQueries);\n if (await isFile(inQueries)) {\n return inQueries;\n }\n\n // 4. queries/<arg>.yml (skip if arg already has extension)\n if (!arg.endsWith('.yaml') && !arg.endsWith('.yml')) {\n const inQueriesYml = `queries/${arg}.yml`;\n candidates.push(inQueriesYml);\n if (await isFile(inQueriesYml)) {\n return inQueriesYml;\n }\n }\n\n // 5. Error\n const tried = [`./${arg}`, ...candidates.map(c => `./${c}`)];\n throw new Error(\n `Query file not found: \"${arg}\"\\n` +\n ` Tried:\\n` +\n tried.map(p => ` ${p}`).join('\\n') + '\\n' +\n ` Create a new query: search-hub query init \"${arg}\"`\n );\n}\n"],"names":[],"mappings":";AAYO,MAAM,sBAAsB,MAAM;AAAA,EACvC,YAAY,MAAc;AACxB,UAAM,uBAAuB,IAAI,EAAE;AACnC,SAAK,OAAO;AAAA,EACd;AACF;AAEA,eAAe,OAAO,MAAgC;AACpD,MAAI;AACF,UAAM,IAAI,MAAM,KAAK,IAAI;AACzB,QAAI,CAAC,EAAE,UAAU;AACf,YAAM,IAAI,cAAc,IAAI;AAAA,IAC9B;AACA,WAAO;AAAA,EACT,SAAS,OAAO;AACd,QAAI,iBAAiB,eAAe;AAClC,YAAM;AAAA,IACR;AACA,WAAO;AAAA,EACT;AACF;AAEA,eAAsB,iBAAiB,KAA8B;AAEnE,MAAI,MAAM,OAAO,GAAG,GAAG;AACrB,WAAO;AAAA,EACT;AAEA,QAAM,aAAuB,CAAA;AAG7B,MAAI,CAAC,IAAI,SAAS,OAAO,KAAK,CAAC,IAAI,SAAS,MAAM,GAAG;AACnD,UAAM,UAAU,GAAG,GAAG;AACtB,eAAW,KAAK,OAAO;AACvB,QAAI,MAAM,OAAO,OAAO,GAAG;AACzB,aAAO;AAAA,IACT;AAAA,EACF;AAGA,QAAM,WAAW,IAAI,SAAS,OAAO,KAAK,IAAI,SAAS,MAAM,IAAI,MAAM,GAAG,GAAG;AAC7E,QAAM,YAAY,WAAW,QAAQ;AACrC,aAAW,KAAK,SAAS;AACzB,MAAI,MAAM,OAAO,SAAS,GAAG;AAC3B,WAAO;AAAA,EACT;AAGA,MAAI,CAAC,IAAI,SAAS,OAAO,KAAK,CAAC,IAAI,SAAS,MAAM,GAAG;AACnD,UAAM,eAAe,WAAW,GAAG;AACnC,eAAW,KAAK,YAAY;AAC5B,QAAI,MAAM,OAAO,YAAY,GAAG;AAC9B,aAAO;AAAA,IACT;AAAA,EACF;AAGA,QAAM,QAAQ,CAAC,KAAK,GAAG,IAAI,GAAG,WAAW,IAAI,CAAA,MAAK,KAAK,CAAC,EAAE,CAAC;AAC3D,QAAM,IAAI;AAAA,IACR,0BAA0B,GAAG;AAAA;AAAA,IAE7B,MAAM,IAAI,CAAA,MAAK,OAAO,CAAC,EAAE,EAAE,KAAK,IAAI,IAAI;AAAA,+CACQ,GAAG;AAAA,EAAA;AAEvD;"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"entry-bun.d.ts","sourceRoot":"","sources":["../../src/cli/entry-bun.ts"],"names":[],"mappings":""}
|
package/dist/cli/index.d.ts.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAyM5C;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,
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1
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+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAQA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAyM5C;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gCAAgC;IAChC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,4BAA4B;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,wCAAwC;IACxC,KAAK,EAAE,OAAO,CAAC;IACf,qEAAqE;IACrE,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,wBAAgB,aAAa,IAAI,OAAO,CA+vFvC;AAED;;GAEG;AACH,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAG1C"}
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