helixlife-expert-cli 0.1.0

package/cli/dist/modules/proposal/constants.js

@@ -0,0 +1,75 @@
+import { helixlifeError, helixlifeErrorCode } from "../../core/index.js";
+export const PROPOSAL_EXPERT_ID = "proposal";
+export const PROPOSAL_EXPERT_TITLE = "课题方案专家";
+/** 三大方向：基础研究走外部 newidea CLI，临床与生信走工作流接口 */
+export const PROPOSAL_DIRECTIONS = [
+    { id: "basic", title: "基础研究", status: "available" },
+    { id: "clinical", title: "临床研究", status: "available" },
+    { id: "bioinfo", title: "生信方案", status: "available" },
+];
+/** 基础研究方向对应的 newidea 工具 ID（固定，不对用户暴露） */
+export const PROPOSAL_BASIC_TOOL_ID = "d77ba6b6-fc59-4747-bede-68fe71da7337";
+// 表单字段由接口实时返回，此处只登记路由所需的静态信息。
+// 五个工作流的 input_Research_Objective 均被锁成单一选项，故 source 即等价于研究目的。
+export const PROPOSAL_CLINICAL_WORKFLOWS = [
+    {
+        source: "diagnostic-study",
+        name: "诊断研究",
+        title: "诊断研究",
+        objective: "诊断",
+        design: "队列研究 / 病例对照研究 / 横断面研究",
+        purpose: "评价诊断方法准确性或构建诊断模型，可选队列、病例对照或横断面设计",
+    },
+    {
+        source: "prognosis-study",
+        name: "预后研究",
+        title: "预后研究",
+        objective: "预后",
+        design: "队列研究 / 临床试验",
+        purpose: "随访观察结局并评估预后因素，可选构建预后模型或做预后评估",
+    },
+    {
+        source: "treatment-trial",
+        name: "疗效临床试验",
+        title: "疗效临床试验",
+        objective: "疗效",
+        design: "临床试验",
+        purpose: "以前瞻性干预试验比较治疗方案疗效",
+    },
+    {
+        source: "etiology-study",
+        name: "病因研究",
+        title: "病因研究",
+        objective: "病因",
+        design: "队列研究",
+        purpose: "前瞻性队列追踪暴露因素与结局的因果关联，支持两组暴露因素",
+    },
+    {
+        source: "treatment-cohort",
+        name: "疗效队列",
+        title: "疗效队列研究",
+        objective: "疗效",
+        design: "队列研究",
+        purpose: "以回顾性或前瞻性队列比较治疗方案疗效，无需随机干预",
+    },
+];
+export const PROPOSAL_CLINICAL_SOURCES = PROPOSAL_CLINICAL_WORKFLOWS.map((item) => item.source);
+export function findClinicalWorkflow(raw) {
+    const value = raw.trim().toLowerCase();
+    return PROPOSAL_CLINICAL_WORKFLOWS.find((item) => item.source === value);
+}
+export function parseClinicalWorkflow(raw) {
+    const workflow = findClinicalWorkflow(raw);
+    if (workflow) {
+        return workflow;
+    }
+    throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无效工作流: ${raw}，可选: ${PROPOSAL_CLINICAL_SOURCES.join(" | ")}`);
+}
+/** 生信方案只有一个工作流，source 固定，不对用户暴露选择 */
+export const PROPOSAL_BIOINFO_WORKFLOW = {
+    source: "bioinfo-planner",
+    name: "生信分析方案设计",
+    title: "生信分析方案",
+    purpose: "围绕疾病与表型需求，产出可执行的生物信息学分析方案",
+};
+//# sourceMappingURL=constants.js.map

package/cli/dist/modules/proposal/constants.js.map

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package/cli/dist/modules/proposal/index.d.ts

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+import type { Command } from "commander";
+export declare function registerProposalCommands(program: Command): void;
+//# sourceMappingURL=index.d.ts.map

package/cli/dist/modules/proposal/index.d.ts.map

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package/cli/dist/modules/proposal/index.js

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+import { emitJson, parseOutputFormat } from "../../core/index.js";
+import { PROPOSAL_BIOINFO_WORKFLOW, PROPOSAL_CLINICAL_SOURCES, PROPOSAL_CLINICAL_WORKFLOWS, PROPOSAL_DIRECTIONS, PROPOSAL_EXPERT_ID, PROPOSAL_EXPERT_TITLE, } from "./constants.js";
+import { runListClinicalWorkflows } from "./commands/clinical-list.js";
+import { runClinicalWorkflowParams } from "./commands/clinical-params.js";
+import { runClinicalWorkflow } from "./commands/clinical-run.js";
+import { runBioinfoWorkflowParams } from "./commands/bioinfo-params.js";
+import { runBioinfoWorkflow } from "./commands/bioinfo-run.js";
+const CLINICAL_SOURCE_HINT = `工作流：${PROPOSAL_CLINICAL_SOURCES.join(" | ")}`;
+// 注册课题方案专家命名空间。
+// 基础研究经外部 newidea CLI（npm: @helixlife-ai/newidea）异步执行；
+// 临床研究与生信方案走「查表单 → 填参执行」两步式工作流命令。
+export function registerProposalCommands(program) {
+    const proposal = program
+        .command(PROPOSAL_EXPERT_ID)
+        .description(PROPOSAL_EXPERT_TITLE);
+    proposal
+        .command("info")
+        .description("查看课题方案专家模块状态与三大方向可用性")
+        .action(() => {
+        emitJson({
+            ok: true,
+            expert: PROPOSAL_EXPERT_ID,
+            title: PROPOSAL_EXPERT_TITLE,
+            implemented: true,
+            directions: PROPOSAL_DIRECTIONS,
+            clinicalWorkflows: PROPOSAL_CLINICAL_WORKFLOWS.map((item) => ({
+                source: item.source,
+                title: item.title,
+                objective: item.objective,
+                design: item.design,
+            })),
+            bioinfoWorkflow: {
+                source: PROPOSAL_BIOINFO_WORKFLOW.source,
+                title: PROPOSAL_BIOINFO_WORKFLOW.title,
+            },
+            note: "基础研究经外部 newidea CLI（npm: @helixlife-ai/newidea）异步执行；临床研究与生信方案由本 CLI 直接调用工作流接口",
+        });
+    });
+    const clinical = proposal
+        .command("clinical")
+        .description("临床研究方案：按研究目的选工作流，查表单后执行");
+    clinical
+        .command("list")
+        .description("列出五个临床研究工作流及其用途")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action((opts) => {
+        runListClinicalWorkflows({ format: parseOutputFormat(opts.format) });
+    });
+    clinical
+        .command("params")
+        .description("查询指定临床工作流的动态表单字段与输出定义")
+        .requiredOption("--source <source>", CLINICAL_SOURCE_HINT)
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runClinicalWorkflowParams({
+            source: opts.source,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    clinical
+        .command("run")
+        .description("按填好的参数生成临床研究方案")
+        .requiredOption("--source <source>", CLINICAL_SOURCE_HINT)
+        .requiredOption("--inputs-file <path>", "JSON 文件 {字段名: 值}")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runClinicalWorkflow({
+            source: opts.source,
+            inputsFile: opts.inputsFile,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const bioinfo = proposal
+        .command("bioinfo")
+        .description("生信分析方案：单一工作流，无需指定 source");
+    bioinfo
+        .command("params")
+        .description("查询生信方案的动态表单字段与输出定义")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runBioinfoWorkflowParams({ format: parseOutputFormat(opts.format) });
+    });
+    bioinfo
+        .command("run")
+        .description("按填好的参数生成生信分析方案")
+        .requiredOption("--inputs-file <path>", "JSON 文件 {字段名: 值}")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runBioinfoWorkflow({
+            inputsFile: opts.inputsFile,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

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package/cli/dist/modules/proposal/newidea-env.d.ts

@@ -0,0 +1,28 @@
+/** newidea 本地配置文件（与 helixlife-expert 的 config.json 分离） */
+export declare const NEWIDEA_CONFIG_RELATIVE_PATH = ".config/newidea/config.json";
+/** newidea 支持的配置项（见 @helixlife-ai/newidea README） */
+export type NewideaConfigKey = "auth-api-url" | "agent-url" | "base-url" | "api-url" | "completion-url" | "diagram-api-url";
+/** 生产默认 invocation 前缀（newidea 包内默认值） */
+export declare const NEWIDEA_DEFAULT_AGENT_URL = "https://agent-service.newidea.pro/api/v1";
+/**
+ * 测试/预发（api.helixlife.net）联调用的 invocation 前缀。
+ * 可通过环境变量 NEWIDEA_AGENT_URL 或 `newidea config set agent-url` 覆盖。
+ */
+export declare const NEWIDEA_TEST_AGENT_URL: string;
+export interface NewideaEnvRecommendation {
+    /** helixlife-expert 当前生效的业务 api */
+    helix_api: string;
+    /** helixlife-expert 当前生效的 agent_api */
+    helix_agent_api: string;
+    profile: "test" | "production" | "custom";
+    newidea_config_path: string;
+    /** 写入 ~/.config/newidea/config.json 的键值 */
+    newidea_config: Partial<Record<NewideaConfigKey, string>>;
+    /** 与 newidea 包一致的环境变量名（优先级高于配置文件） */
+    env_vars: Record<string, string>;
+    setup_commands: string[];
+    notes: string[];
+}
+/** 根据 helixlife-expert 当前 api/agent_api 生成 newidea 应对齐的独立配置建议 */
+export declare function getNewideaEnvRecommendation(): NewideaEnvRecommendation;
+//# sourceMappingURL=newidea-env.d.ts.map

package/cli/dist/modules/proposal/newidea-env.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/proposal/newidea-env.js

@@ -0,0 +1,69 @@
+import { getDefaultAuthBaseUrl, getDefaultBaseUrl } from "../../core/index.js";
+/** newidea 本地配置文件（与 helixlife-expert 的 config.json 分离） */
+export const NEWIDEA_CONFIG_RELATIVE_PATH = ".config/newidea/config.json";
+/** 与 helixlife-expert `api` 基址对齐的 newidea `auth-api-url` 建议值 */
+const AUTH_API_BY_HELIX_API = {
+    "https://api.helixlife.net": "https://agent.helixlife.net/api/v1",
+    "https://api.helixlife.cn": "https://agent.helixlife.cn/api/v1",
+};
+/** 生产默认 invocation 前缀（newidea 包内默认值） */
+export const NEWIDEA_DEFAULT_AGENT_URL = "https://agent-service.newidea.pro/api/v1";
+/**
+ * 测试/预发（api.helixlife.net）联调用的 invocation 前缀。
+ * 可通过环境变量 NEWIDEA_AGENT_URL 或 `newidea config set agent-url` 覆盖。
+ */
+export const NEWIDEA_TEST_AGENT_URL = process.env.NEWIDEA_TEST_AGENT_URL?.trim() ||
+    process.env.NEWIDEA_AGENT_URL?.trim() ||
+    NEWIDEA_DEFAULT_AGENT_URL;
+function normalizeBase(url) {
+    return url.trim().replace(/\/+$/, "");
+}
+function resolveProfile(helixApi) {
+    if (helixApi.includes("helixlife.net")) {
+        return "test";
+    }
+    if (helixApi.includes("helixlife.cn")) {
+        return "production";
+    }
+    return "custom";
+}
+/** 根据 helixlife-expert 当前 api/agent_api 生成 newidea 应对齐的独立配置建议 */
+export function getNewideaEnvRecommendation() {
+    const helixApi = normalizeBase(getDefaultBaseUrl());
+    const helixAgentApi = normalizeBase(getDefaultAuthBaseUrl());
+    const profile = resolveProfile(helixApi);
+    const authApiUrl = AUTH_API_BY_HELIX_API[helixApi] ??
+        `${helixAgentApi}/api/v1`.replace(/\/api\/v1\/api\/v1$/, "/api/v1");
+    const agentUrl = profile === "test" ? NEWIDEA_TEST_AGENT_URL : NEWIDEA_DEFAULT_AGENT_URL;
+    const newidea_config = {
+        "auth-api-url": authApiUrl,
+        "agent-url": agentUrl,
+    };
+    const env_vars = {
+        HELIXLIFE_AUTH_API_URL: authApiUrl,
+        NEWIDEA_AGENT_URL: agentUrl,
+    };
+    const setup_commands = [
+        `newidea config set auth-api-url ${authApiUrl}`,
+        `newidea config set agent-url ${agentUrl}`,
+    ];
+    const notes = [
+        "newidea 不读取 ~/.config/helixlife/config.json；仅共用 user-access-token.txt。",
+        "newidea 配置写入 ~/.config/newidea/config.json，或使用 HELIXLIFE_AUTH_API_URL / NEWIDEA_AGENT_URL 等环境变量（优先级更高）。",
+        "修改 helixlife-expert 的 api/agent_api 不会自动同步 newidea，需按本建议单独设置。",
+    ];
+    if (profile === "test") {
+        notes.push("测试 token（api.helixlife.net）与生产 invocation 网关的鉴权体系可能不一致；若 invocation start 仍报 Token 无效，需后台提供测试环境 agent-url 或开通网关认测试 token。");
+    }
+    return {
+        helix_api: helixApi,
+        helix_agent_api: helixAgentApi,
+        profile,
+        newidea_config_path: NEWIDEA_CONFIG_RELATIVE_PATH,
+        newidea_config,
+        env_vars,
+        setup_commands,
+        notes,
+    };
+}
+//# sourceMappingURL=newidea-env.js.map

package/cli/dist/modules/proposal/newidea-env.js.map

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package/cli/dist/modules/proposal/newidea-runner.d.ts

@@ -0,0 +1,25 @@
+export declare const NEWIDEA_PACKAGE = "@helixlife-ai/newidea";
+export interface NewideaRunner {
+    /** 始终为当前 node 可执行文件，避免 Windows 上 .cmd/.ps1 shim 必须走 shell */
+    execPath: string;
+    /** 业务参数前的固定前缀：[run.js] 或 [npx-cli.js, --yes, <pkg>] */
+    baseArgs: string[];
+    /** 解析来源，写入结果供排查 */
+    via: string;
+}
+/**
+ * 解析 newidea 可执行入口，按序：环境变量覆盖 → 已装（全局/本地）→ 自动全局安装 → npx 兜底。
+ * 结果在进程内缓存，一次命令里只解析一次。
+ */
+export declare function resolveNewideaRunner(): Promise<NewideaRunner>;
+/** 仅供测试重置解析缓存 */
+export declare function __resetNewideaRunnerForTesting(): void;
+export interface RunNewideaOptions {
+    timeoutMs?: number;
+}
+/**
+ * 执行一条 newidea 命令并解析其 --json 输出。
+ * 非零退出时若 stdout 仍带 JSON（CLI 的结构化报错），优先返回该 JSON 交上层判断。
+ */
+export declare function runNewideaJson(args: string[], options?: RunNewideaOptions): Promise<unknown>;
+//# sourceMappingURL=newidea-runner.d.ts.map

package/cli/dist/modules/proposal/newidea-runner.d.ts.map

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package/cli/dist/modules/proposal/newidea-runner.js

@@ -0,0 +1,158 @@
+/**
+ * newidea CLI 调用层
+ *
+ * 课题方案基础研究走外部 newidea 异步任务。用户输入的课题条件会作为参数传入，
+ * 因此主路径一律用 `node <run.js> ...` + 参数数组、shell: false 执行，
+ * 不经 shell 解析，规避命令注入。
+ */
+import { exec, execFile } from "node:child_process";
+import { existsSync } from "node:fs";
+import { join } from "node:path";
+import { promisify } from "node:util";
+import { helixlifeError, helixlifeErrorCode } from "../../core/index.js";
+import { extractJsonFromStdout } from "./parse.js";
+const execFileAsync = promisify(execFile);
+// npm 在 Windows 上是 .cmd shim，必须经 shell；以下 npm 命令全为常量字符串，无注入面
+const execAsync = promisify(exec);
+export const NEWIDEA_PACKAGE = "@helixlife-ai/newidea";
+const NEWIDEA_BIN_RELATIVE = join("@helixlife-ai", "newidea", "bin", "run.js");
+const NPX_CLI_RELATIVE = join("npm", "bin", "npx-cli.js");
+const DEFAULT_EXEC_TIMEOUT_MS = 600_000;
+const MAX_STDOUT_BYTES = 20 * 1024 * 1024;
+let cachedRunner = null;
+async function readNpmRoot(global) {
+    try {
+        const { stdout } = await execAsync(global ? "npm root -g" : "npm root", {
+            encoding: "utf-8",
+            windowsHide: true,
+            timeout: 60_000,
+        });
+        const dir = stdout.trim();
+        return dir || null;
+    }
+    catch {
+        return null;
+    }
+}
+async function findRunJs() {
+    const globalRoot = await readNpmRoot(true);
+    if (globalRoot) {
+        const candidate = join(globalRoot, NEWIDEA_BIN_RELATIVE);
+        if (existsSync(candidate)) {
+            return { path: candidate, via: "global" };
+        }
+    }
+    const localRoot = await readNpmRoot(false);
+    if (localRoot) {
+        const candidate = join(localRoot, NEWIDEA_BIN_RELATIVE);
+        if (existsSync(candidate)) {
+            return { path: candidate, via: "local" };
+        }
+    }
+    return null;
+}
+async function installNewideaGlobally() {
+    await execAsync(`npm install -g ${NEWIDEA_PACKAGE}@latest`, {
+        encoding: "utf-8",
+        windowsHide: true,
+        timeout: 300_000,
+    });
+}
+async function findNpxCli() {
+    const globalRoot = await readNpmRoot(true);
+    if (!globalRoot) {
+        return null;
+    }
+    const candidate = join(globalRoot, NPX_CLI_RELATIVE);
+    return existsSync(candidate) ? candidate : null;
+}
+/**
+ * 解析 newidea 可执行入口，按序：环境变量覆盖 → 已装（全局/本地）→ 自动全局安装 → npx 兜底。
+ * 结果在进程内缓存，一次命令里只解析一次。
+ */
+export async function resolveNewideaRunner() {
+    if (cachedRunner) {
+        return cachedRunner;
+    }
+    const override = process.env.HELIXLIFE_NEWIDEA_BIN?.trim();
+    if (override) {
+        if (!existsSync(override)) {
+            throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `HELIXLIFE_NEWIDEA_BIN 指向的文件不存在：${override}`);
+        }
+        cachedRunner = {
+            execPath: process.execPath,
+            baseArgs: [override],
+            via: "env",
+        };
+        return cachedRunner;
+    }
+    let found = await findRunJs();
+    if (!found) {
+        // 被动安装：仅在确实缺失时才装，不在会话开始预装
+        try {
+            await installNewideaGlobally();
+        }
+        catch {
+            // 安装失败继续走 npx 兜底
+        }
+        found = await findRunJs();
+    }
+    if (found) {
+        cachedRunner = {
+            execPath: process.execPath,
+            baseArgs: [found.path],
+            via: found.via,
+        };
+        return cachedRunner;
+    }
+    const npxCli = await findNpxCli();
+    if (npxCli) {
+        cachedRunner = {
+            execPath: process.execPath,
+            baseArgs: [npxCli, "--yes", `${NEWIDEA_PACKAGE}@latest`],
+            via: "npx",
+        };
+        return cachedRunner;
+    }
+    throw new helixlifeError(helixlifeErrorCode.REQUEST_FAILED, `未找到 ${NEWIDEA_PACKAGE}，请手动执行 npm install -g ${NEWIDEA_PACKAGE}@latest 后重试（或用 HELIXLIFE_NEWIDEA_BIN 指定 bin/run.js 路径）`);
+}
+/** 仅供测试重置解析缓存 */
+export function __resetNewideaRunnerForTesting() {
+    cachedRunner = null;
+}
+/**
+ * 执行一条 newidea 命令并解析其 --json 输出。
+ * 非零退出时若 stdout 仍带 JSON（CLI 的结构化报错），优先返回该 JSON 交上层判断。
+ */
+export async function runNewideaJson(args, options = {}) {
+    const runner = await resolveNewideaRunner();
+    const timeout = options.timeoutMs ?? DEFAULT_EXEC_TIMEOUT_MS;
+    try {
+        const { stdout } = await execFileAsync(runner.execPath, [...runner.baseArgs, ...args], {
+            encoding: "utf-8",
+            windowsHide: true,
+            timeout,
+            maxBuffer: MAX_STDOUT_BYTES,
+        });
+        return extractJsonFromStdout(stdout);
+    }
+    catch (error) {
+        const stdout = typeof error?.stdout === "string"
+            ? error.stdout
+            : "";
+        if (stdout.trim()) {
+            try {
+                return extractJsonFromStdout(stdout);
+            }
+            catch {
+                // 落到统一错误
+            }
+        }
+        const stderr = typeof error?.stderr === "string"
+            ? error.stderr.trim()
+            : "";
+        const message = stderr || (error instanceof Error ? error.message : String(error));
+        throw new helixlifeError(helixlifeErrorCode.REQUEST_FAILED, `newidea 命令执行失败：${message}`, { cause: error });
+    }
+}
+//# sourceMappingURL=newidea-runner.js.map

package/cli/dist/modules/proposal/newidea-runner.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/proposal/parse.d.ts

@@ -0,0 +1,25 @@
+/** 归一后的任务状态：未知状态一律按 running 处理，避免误判为失败而中断轮询 */
+export type InvocationStatus = "running" | "success" | "failed";
+export interface NormalizedInvocationProcess {
+    status: InvocationStatus;
+    /** 接口原始 status，保留供排查 */
+    rawStatus: string;
+    error: string | null;
+    /** 产物 ZIP 直链；成功也可能为 null */
+    artifacts: string | null;
+    itemCount: number;
+}
+/**
+ * 从 CLI stdout 中提取首个完整 JSON 值（对象或数组）。
+ */
+export declare function extractJsonFromStdout(stdout: string): unknown;
+/**
+ * 从 `invocation start` / `last` 的返回中提取 run_record_id。
+ * 兼容下划线与驼峰，并向下一层 data / record / result 探一层。
+ */
+export declare function parseRunRecordId(raw: unknown): string | undefined;
+/**
+ * 归一 `invocation process` 返回：状态、错误、产物链接与事件条数。
+ */
+export declare function normalizeInvocationProcess(raw: unknown): NormalizedInvocationProcess;
+//# sourceMappingURL=parse.d.ts.map

package/cli/dist/modules/proposal/parse.d.ts.map

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