@helixlife-ai/xiantao 0.1.12 → 0.1.14

package/README.md

@@ -36,10 +36,13 @@ This starts a menu-driven path for choosing a tool, selecting demo data or a loc
 ```bash
 xt tool prepare violin_flat --file ./data.xlsx --profile opencode --json
 xt tool exec violin_flat --file ./data.xlsx --profile opencode --json
+xt tool exec violin_flat --file ./data.xlsx --profile opencode --json --download ./violin.pdf
 ```
 
 For machine callers, use `xt tool prepare` to fetch the upload-dependent final schema, then `xt tool exec` to submit. Keep `--json`, pass an explicit profile with `--profile`, and avoid interactive-only flows.
 
+For agent workflows, do not use `xt tool run`. Treat `xt tool run` as the human-first path and `xt tool exec` as the machine path.
+
 `xt login --json` now returns the authorization link immediately and defaults to `authorized: false` until the browser step completes. Use `xt login --json --wait` when you explicitly want the command to block until authorization is confirmed. `xt status` is a probe-style check and returns `authorized: true` or `authorized: false` together with a reason such as `missing_token` or `expired_token`.
 
 ## Command Groups
@@ -71,7 +74,9 @@ For machine callers, use `xt tool prepare` to fetch the upload-dependent final s
 
 For the common Xiantao tool product, `tool search`, `tool inspect`, `tool run`, `tool resolve`, and `tool menu` default `toolProductUuid` to `c0b6febb-52dd-4525-970a-61bbe9e263ff`. You can override it with `--toolProductUuid`, `XIANTAO_TOOL_PRODUCT_UUID`, or `~/.config/xtz/config.json` under `xiantao.toolProductUuid`.
 
-`xt tool search <keyword>` searches remote tool menus by tool id, title, path, and route. `xt tool inspect <tool_id>` prints resolved metadata together with the dynamic `args_main` schema used by the tool. `xt tool run <tool_id>` runs a Xiantao bioinformatics tool. `xt tool resolve <tool_id>` remains available as the low-level UUID and route lookup. `--demo` reuses the demo file metadata returned by `tool fetch-all`; otherwise `tool run` uploads the local file first and therefore also needs token auth. Run `xt login` first to authorize the stored token. When a tool exposes multiple downloadable results, `--download <path>` uses the output file extension to select the matching artifact.
+The CLI also loads a project-root `.env` file on startup. You can set `XIANTAO_BASE_URL=https://agent.helixlife.cn` there to switch the API base URL without prefixing each command manually.
+
+`xt tool search <keyword>` searches remote tool menus by tool id, title, path, and route. `xt tool inspect <tool_id>` prints resolved metadata together with the dynamic `args_main` schema used by the tool. `xt tool run <tool_id>` runs a Xiantao bioinformatics tool in the human-first path. `xt tool exec <tool_id>` is the agent-safe submit command and also supports `--download <path>` when a local artifact is needed. `xt tool resolve <tool_id>` remains available as the low-level UUID and route lookup. `--demo` reuses the demo file metadata returned by `tool fetch-all`; otherwise `tool run` uploads the local file first and therefore also needs token auth. Run `xt login` first to authorize the stored token. When a tool exposes multiple downloadable results, `--download <path>` uses the output file extension to select the matching artifact.
 
 `xt tool run <tool_id> ... --interactive` prompts for dynamic `args_main` values before the final submit, prints reusable `--set` flags, and supports `<` for the previous item plus `/skip` for the current section.
 

package/bin/dev.js

@@ -1,5 +1,7 @@
 #!/usr/bin/env node
 
 import {execute} from '@oclif/core'
+import {loadProjectEnv} from './load-env.js'
 
+loadProjectEnv()
 await execute({development: true, dir: import.meta.url})

package/bin/load-env.js

@@ -0,0 +1,12 @@
+import path from 'node:path'
+import {loadEnvFile} from 'node:process'
+
+export function loadProjectEnv() {
+  try {
+    loadEnvFile(path.join(process.cwd(), '.env'))
+  } catch (error) {
+    if (error?.code !== 'ENOENT') {
+      throw error
+    }
+  }
+}

package/bin/run.js

@@ -1,5 +1,7 @@
 #!/usr/bin/env node
 
 import {execute} from '@oclif/core'
+import {loadProjectEnv} from './load-env.js'
 
+loadProjectEnv()
 await execute({dir: import.meta.url})

package/dist/commands/tool/exec.js

@@ -6,7 +6,7 @@ import { plotOverrideFlags } from '../../lib/plot-options.js';
 import { ToolRunCommandBase } from '../plot/run.js';
 export default class ToolExec extends ToolRunCommandBase {
     static description = 'Execute a Xiantao bioinformatics tool in agent mode';
-    static usage = 'tool exec <tool> (--file <value> | --demo) --json';
+    static usage = 'tool exec <tool> (--file <value> | --demo) --json [--download <path>]';
     static args = {
         tool: Args.string({
             description: 'Tool id, e.g. violin_flat',
@@ -24,7 +24,7 @@ export default class ToolExec extends ToolRunCommandBase {
             description: 'Use the module demo data returned by fetch-all instead of uploading a local file',
         }),
         download: Flags.string({
-            hidden: true,
+            description: 'Download the generated file or preferred analysis result to this local path after submission',
         }),
         file: Flags.string({
             description: 'Path to the local xlsx file',
@@ -71,7 +71,6 @@ export default class ToolExec extends ToolRunCommandBase {
         }
         const result = await this.executeToolRun(args.tool, filePath, {
             ...flags,
-            download: undefined,
             interactive: false,
         });
         const profile = await this.getProfile(flags.profile);

package/dist/lib/constants.js

@@ -1,10 +1,11 @@
 export const DEFAULT_AGENT = 'opencode';
 export const XTZ_CONFIG_PATH = '.config/xtz/config.json';
 export const XTZ_UPDATE_CHECK_PATH = '.config/xtz/update-check.json';
-export const AUTH_URL_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/skills/auth-url';
-export const XIANTAO_BIO_API_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/bio-api';
-export const XIANTAO_TOOL_MENUS_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/tool/menus';
+export const XIANTAO_BASE_URL = (process.env.XIANTAO_BASE_URL?.trim() || 'https://agent.helixlife.net').replace(/\/+$/, '');
+export const AUTH_URL_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/skills/auth-url`;
+export const XIANTAO_BIO_API_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/bio-api`;
+export const XIANTAO_TOOL_MENUS_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/tool/menus`;
 export const DEFAULT_XIANTAO_TOOL_PRODUCT_UUID = 'c0b6febb-52dd-4525-970a-61bbe9e263ff';
-export const CHECK_TOKEN_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/skills/check-token';
-export const UPLOAD_CONFIG_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/upload/config?type=bio&oss_type=bio';
-export const BIO_API_ENDPOINT = 'https://agent.helixlife.net/api/v1/agent/bio-api';
+export const CHECK_TOKEN_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/skills/check-token`;
+export const UPLOAD_CONFIG_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/upload/config?type=bio&oss_type=bio`;
+export const BIO_API_ENDPOINT = `${XIANTAO_BASE_URL}/api/v1/agent/bio-api`;

package/dist/lib/xiantao.js

@@ -1,4 +1,4 @@
-import { XIANTAO_BIO_API_ENDPOINT, XIANTAO_TOOL_MENUS_ENDPOINT } from './constants.js';
+import { XIANTAO_BASE_URL, XIANTAO_BIO_API_ENDPOINT, XIANTAO_TOOL_MENUS_ENDPOINT } from './constants.js';
 import { XtzError } from './errors.js';
 import { requestJson } from './http.js';
 export async function fetchToolMenu(auth, menuUuid, toolProductUuid) {
@@ -156,9 +156,9 @@ function encodeMenuFilter(filter) {
 export function buildXiantaoHeaders(auth, hasJsonBody = false) {
     const headers = {
         Authorization: `Bearer ${auth.token}`,
-        origin: 'https://agent.helixlife.net',
+        origin: XIANTAO_BASE_URL,
         platform: 'pc',
-        referer: 'https://agent.helixlife.net',
+        referer: XIANTAO_BASE_URL,
         source: 'PC',
     };
     if (hasJsonBody) {

package/dist/xtz-help.js

@@ -35,11 +35,11 @@ export default class XtzHelp extends Help {
                 id: 'tool:inspect',
             },
             {
-                description: 'Run a tool in human-first mode',
+                description: 'Run a tool in human-first mode; avoid this in agent workflows',
                 id: 'tool:run',
             },
             {
-                description: 'Execute a tool in agent mode with JSON envelope output',
+                description: 'Execute a tool in agent mode with JSON envelope output; supports --download',
                 id: 'tool:exec',
             },
             {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@helixlife-ai/xiantao",
-  "version": "0.1.12",
+  "version": "0.1.14",
   "description": "CLI for Xiantao bioinformatics tools",
   "type": "module",
   "main": "dist/index.js",