helixlife-expert-cli 0.1.0

package/cli/dist/core/types/config.js

@@ -0,0 +1,30 @@
+import { loadLocalConfig } from "../env-config.js";
+// 生产默认地址：本地 config.json 缺失对应字段时回退至此。
+// 覆盖方式：`helixlife-expert config set api|agent_api <完整基址>` 写入 ~/.config/helixlife/config.json。
+const DEFAULT_ENDPOINTS = {
+    api: "https://api.helixlife.cn",
+    agent_api: "https://agent.helixlife.cn",
+    newidea: "https://paas-api.newidea.pro",
+};
+// 解析当前生效基址：本地有对应字段则原样使用，否则回退生产默认。
+function resolveEndpoints() {
+    const local = loadLocalConfig();
+    return {
+        api: local?.api || DEFAULT_ENDPOINTS.api,
+        agent_api: local?.agent_api || DEFAULT_ENDPOINTS.agent_api,
+        newidea: DEFAULT_ENDPOINTS.newidea,
+    };
+}
+// 业务主接口基址：每次取用前重读本地配置
+export function getDefaultBaseUrl() {
+    return resolveEndpoints().api;
+}
+// 授权相关接口基址：每次取用前重读本地配置
+export function getDefaultAuthBaseUrl() {
+    return resolveEndpoints().agent_api;
+}
+// Newidea PaaS 平台接口基址（固定，不读本地配置）
+export function getDefaultNewideaBaseUrl() {
+    return resolveEndpoints().newidea;
+}
+//# sourceMappingURL=config.js.map

package/cli/dist/core/types/config.js.map

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package/cli/dist/core/version.d.ts

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+export declare function getPackageVersion(): string;
+//# sourceMappingURL=version.d.ts.map

package/cli/dist/core/version.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/core/version.js

@@ -0,0 +1,10 @@
+import { readFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+// 从 package.json 读取版本号，避免与 index.ts 硬编码重复
+export function getPackageVersion() {
+    const pkgPath = join(dirname(fileURLToPath(import.meta.url)), "../../../package.json");
+    const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
+    return pkg.version;
+}
+//# sourceMappingURL=version.js.map

package/cli/dist/core/version.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../../src/core/version.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AAEzC,0CAA0C;AAC1C,MAAM,UAAU,iBAAiB;IAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,uBAAuB,CAAC,CAAC;IACvF,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAwB,CAAC;IAC9E,OAAO,GAAG,CAAC,OAAO,CAAC;AACrB,CAAC"}

package/cli/dist/index.d.ts

@@ -0,0 +1,2 @@
+export { createProgram } from "./program.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC"}

package/cli/dist/index.js

@@ -0,0 +1,23 @@
+import { helixlifeError } from "./core/index.js";
+import { createProgram } from "./program.js";
+export { createProgram } from "./program.js";
+// CLI 入口：解析参数并统一处理错误
+async function main() {
+    const program = createProgram();
+    try {
+        await program.parseAsync(process.argv);
+    }
+    catch (error) {
+        if (error instanceof helixlifeError) {
+            console.error(`[${error.code}] ${error.message}`);
+            process.exit(1);
+        }
+        if (error instanceof Error) {
+            console.error(`[E9999] ${error.message}`);
+            process.exit(1);
+        }
+        throw error;
+    }
+}
+main();
+//# sourceMappingURL=index.js.map

package/cli/dist/index.js.map

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package/cli/dist/modules/analysis/constants.d.ts

@@ -0,0 +1,3 @@
+export declare const ANALYSIS_EXPERT_ID = "analysis";
+export declare const ANALYSIS_EXPERT_TITLE = "\u6570\u636E\u5206\u6790\u4E13\u5BB6";
+//# sourceMappingURL=constants.d.ts.map

package/cli/dist/modules/analysis/constants.d.ts.map

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

@@ -0,0 +1,3 @@
+export const ANALYSIS_EXPERT_ID = "analysis";
+export const ANALYSIS_EXPERT_TITLE = "数据分析专家";
+//# sourceMappingURL=constants.js.map

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

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

@@ -0,0 +1,3 @@
+import type { Command } from "commander";
+export declare function registerAnalysisCommands(program: Command): void;
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/modules/analysis/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAMzC,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAkB/D"}

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

@@ -0,0 +1,23 @@
+import { emitJson } from "../../core/index.js";
+import { ANALYSIS_EXPERT_ID, ANALYSIS_EXPERT_TITLE } from "./constants.js";
+// 注册数据分析专家命名空间：helixlife-expert analysis info
+// 业务执行经外部仙桃 CLI（xt，npm: @helixlife-ai/xiantao），与本 CLI 共用 ~/.config/helixlife 授权
+export function registerAnalysisCommands(program) {
+    const analysis = program
+        .command(ANALYSIS_EXPERT_ID)
+        .description(ANALYSIS_EXPERT_TITLE);
+    analysis
+        .command("info")
+        .description("查看数据分析专家模块状态")
+        .action(() => {
+        emitJson({
+            ok: true,
+            expert: ANALYSIS_EXPERT_ID,
+            title: ANALYSIS_EXPERT_TITLE,
+            implemented: true,
+            runtime: "external",
+            note: "分析/绘图经外部仙桃 CLI（xt，npm: @helixlife-ai/xiantao）执行，与本 CLI 共用 ~/.config/helixlife 授权",
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/cli/dist/modules/analysis/index.js.map

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

@@ -0,0 +1,3 @@
+import type { Command } from "commander";
+export declare function registerAuthCommands(program: Command): void;
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
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package/cli/dist/modules/auth/index.js

@@ -0,0 +1,76 @@
+import { checkToken, reauthorize, loadTokenFromFile, clearTokenFile, emitJson, } from "../../core/index.js";
+// 注册授权与鉴权命名空间：helixlife-expert auth status / login / logout
+export function registerAuthCommands(program) {
+    const auth = program.command("auth").description("授权与鉴权管理");
+    auth
+        .command("status")
+        .description("检测本地 token 的授权状态（调用检测授权接口 check-token）")
+        .action(async () => {
+        const token = loadTokenFromFile();
+        if (!token) {
+            emitJson({
+                authorized: false,
+                status: "no_token",
+                message: "本地无 token，请运行 `helixlife-expert auth login` 获取授权链接并完成授权",
+            });
+            process.exitCode = 2;
+            return;
+        }
+        // 未授权时 checkToken 内部已统一清除本地失效 token，命令层无需重复处理
+        const result = await checkToken(token);
+        if (result.status === "valid") {
+            emitJson({
+                authorized: true,
+                status: "valid",
+                message: result.message,
+            });
+            return;
+        }
+        if (result.status === "unauthorized") {
+            emitJson({
+                authorized: false,
+                status: "unauthorized",
+                code: result.code,
+                message: `${result.message}，请运行 \`helixlife-expert auth login\` 重新授权`,
+            });
+            process.exitCode = 2;
+            return;
+        }
+        // error：其他错误（网络 / 权限 / 账号异常等）仅提示，不引导重新授权
+        emitJson({
+            authorized: false,
+            status: "error",
+            code: result.code,
+            message: result.message,
+        });
+        process.exitCode = 3;
+    });
+    auth
+        .command("login")
+        .description("获取授权链接并自动打开浏览器，引导用户完成授权")
+        .option("--no-open", "不自动打开浏览器，仅输出授权链接")
+        .action(async (opts) => {
+        // 始终重新授权：先清除本地失效 token，再获取授权链接，
+        // 避免未绑定的新 token 覆盖有效旧 token 造成「假登录」
+        const result = await reauthorize({
+            openBrowser: opts.open,
+        });
+        emitJson({
+            action: "authorize",
+            token_saved: true,
+            auth_url: result.finalUrl,
+            browser_opened: result.browserOpened,
+            message: result.browserOpened
+                ? "已打开浏览器，请完成授权；完成后运行 `helixlife-expert auth status` 确认授权是否成功。"
+                : "请手动复制 auth_url 到浏览器完成授权；完成后运行 `helixlife-expert auth status` 确认授权是否成功。",
+        });
+    });
+    auth
+        .command("logout")
+        .description("清除本地 token")
+        .action(() => {
+        clearTokenFile();
+        emitJson({ action: "logout", message: "已清除本地 token" });
+    });
+}
+//# sourceMappingURL=index.js.map

package/cli/dist/modules/auth/index.js.map

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package/cli/dist/modules/expert-scaffold.d.ts

@@ -0,0 +1,27 @@
+import type { Command } from "commander";
+export interface ExpertDefinition {
+    id: string;
+    title: string;
+}
+export declare const EXPERTS: readonly [{
+    readonly id: "meta";
+    readonly title: "Meta分析专家";
+}, {
+    readonly id: "fund";
+    readonly title: "基金写作专家";
+}, {
+    readonly id: "sci";
+    readonly title: "SCI写作专家";
+}, {
+    readonly id: "analysis";
+    readonly title: "数据分析专家";
+}, {
+    readonly id: "literature";
+    readonly title: "文献调研专家";
+}, {
+    readonly id: "proposal";
+    readonly title: "课题方案专家";
+}];
+export type ExpertId = (typeof EXPERTS)[number]["id"];
+export declare function registerExpertScaffold(program: Command, expert: ExpertDefinition): void;
+//# sourceMappingURL=expert-scaffold.d.ts.map

package/cli/dist/modules/expert-scaffold.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/expert-scaffold.js

@@ -0,0 +1,25 @@
+import { emitJson } from "../core/index.js";
+export const EXPERTS = [
+    { id: "meta", title: "Meta分析专家" },
+    { id: "fund", title: "基金写作专家" },
+    { id: "sci", title: "SCI写作专家" },
+    { id: "analysis", title: "数据分析专家" },
+    { id: "literature", title: "文献调研专家" },
+    { id: "proposal", title: "课题方案专家" },
+];
+// 注册专家脚手架命名空间：helixlife-expert <id> info
+export function registerExpertScaffold(program, expert) {
+    const cmd = program.command(expert.id).description(expert.title);
+    cmd
+        .command("info")
+        .description(`查看${expert.title}模块状态（脚手架）`)
+        .action(() => {
+        emitJson({
+            ok: true,
+            expert: expert.id,
+            title: expert.title,
+            implemented: false,
+        });
+    });
+}
+//# sourceMappingURL=expert-scaffold.js.map

package/cli/dist/modules/expert-scaffold.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/apps.d.ts

@@ -0,0 +1,19 @@
+/** 临床工作流 execute body：网页所有步骤均不携带订单字段 */
+export interface ClinicalWorkflowBody {
+    response_mode: "streaming";
+    query: string;
+    inputs: Record<string, unknown>;
+    app_id: string;
+    app_name: string;
+    app_mode: "workflow";
+    app_type: 0 | 1;
+}
+/** 对齐 fetchAIOutputs/helixAiRequest 的请求体 */
+export declare function buildClinicalWorkflowBody(params: {
+    query?: string;
+    inputs: Record<string, unknown>;
+    appId: string;
+    appName: string;
+    appType?: 0 | 1;
+}): ClinicalWorkflowBody;
+//# sourceMappingURL=apps.d.ts.map

package/cli/dist/modules/fund/clinical/apps.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/apps.js

@@ -0,0 +1,14 @@
+// 临床工作台 /apps/execute 请求体，对齐网页 fetchAIOutputs/helixAiRequest。
+/** 对齐 fetchAIOutputs/helixAiRequest 的请求体 */
+export function buildClinicalWorkflowBody(params) {
+    return {
+        response_mode: "streaming",
+        query: params.query ?? "",
+        inputs: params.inputs,
+        app_id: params.appId,
+        app_name: params.appName,
+        app_mode: "workflow",
+        app_type: params.appType ?? 1,
+    };
+}
+//# sourceMappingURL=apps.js.map

package/cli/dist/modules/fund/clinical/apps.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/command-utils.d.ts

@@ -0,0 +1,4 @@
+export declare function readClinicalJsonObject(path: string, label: string): Promise<Record<string, unknown>>;
+export declare function readClinicalStringMap(path: string, label: string): Promise<Record<string, string>>;
+export declare function readClinicalTextFile(path: string, label: string): Promise<string>;
+//# sourceMappingURL=command-utils.d.ts.map

package/cli/dist/modules/fund/clinical/command-utils.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/command-utils.js

@@ -0,0 +1,40 @@
+import { readFile } from "node:fs/promises";
+import { helixlifeError, helixlifeErrorCode, resolveUserPath, } from "../../../core/index.js";
+function windowsTempPathHint(path, error) {
+    const code = error?.code;
+    if (process.platform === "win32" &&
+        code === "ENOENT" &&
+        /^\/(?:var\/)?tmp(?:\/|$)/i.test(path.replace(/\\/g, "/"))) {
+        return "；Windows 下请将临时文件写入 %TEMP% 并传入绝对路径，不要使用沙箱 /tmp 路径";
+    }
+    return "";
+}
+export async function readClinicalJsonObject(path, label) {
+    try {
+        const raw = (await readFile(resolveUserPath(path), "utf8")).replace(/^\uFEFF/, "");
+        const parsed = JSON.parse(raw);
+        if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+            throw new Error("JSON 顶层必须是对象");
+        }
+        return parsed;
+    }
+    catch (error) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取${label}: ${error.message}${windowsTempPathHint(path, error)}`);
+    }
+}
+export async function readClinicalStringMap(path, label) {
+    const record = await readClinicalJsonObject(path, label);
+    return Object.fromEntries(Object.entries(record).map(([key, value]) => [
+        key,
+        value === undefined || value === null ? "" : String(value),
+    ]));
+}
+export async function readClinicalTextFile(path, label) {
+    try {
+        return (await readFile(resolveUserPath(path), "utf8")).replace(/^\uFEFF/, "");
+    }
+    catch (error) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, `无法读取${label}: ${error.message}${windowsTempPathHint(path, error)}`);
+    }
+}
+//# sourceMappingURL=command-utils.js.map

package/cli/dist/modules/fund/clinical/command-utils.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/article-create.d.ts

@@ -0,0 +1,9 @@
+import { type OutputFormat } from "../../../../core/index.js";
+export interface CreateClinicalArticleOptions {
+    sessionId?: string;
+    format?: OutputFormat;
+}
+/** 对齐网页 Proofread：text → output → 非 reference 字符串。 */
+export declare function pickClinicalFulltext(outputs: Record<string, unknown> | undefined, streamedText?: string): string;
+export declare function runCreateClinicalArticle(options: CreateClinicalArticleOptions): Promise<void>;
+//# sourceMappingURL=article-create.d.ts.map

package/cli/dist/modules/fund/clinical/commands/article-create.d.ts.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/article-create.js

@@ -0,0 +1,99 @@
+import { createFormatLogger, extractReferences, helixlifeError, helixlifeErrorCode, printOutput, } from "../../../../core/index.js";
+import { wrapWorkbenchResult } from "../../../shared/result-wrapper.js";
+import { CLINICAL_EXECUTE_API_PATH, CLINICAL_FULLTEXT_WAIT_HINT, CLINICAL_WORKFLOW_APP_TYPE, getClinicalFulltextAppId, } from "../constants.js";
+import { fourElementsDraftToWorkflowInputs, isFourElementsDraftDrifted, preprocessClinicalMarkdown, } from "../four-elements.js";
+import { buildClinicalWorkflowBody } from "../apps.js";
+import { streamClinicalWorkflow } from "../sse-utils.js";
+import { requireClinicalSession, updateClinicalSession, } from "../session-cache.js";
+/** 对齐网页 Proofread：text → output → 非 reference 字符串。 */
+export function pickClinicalFulltext(outputs, streamedText = "") {
+    if (outputs) {
+        if (typeof outputs.text === "string" && outputs.text.trim()) {
+            return outputs.text;
+        }
+        if (typeof outputs.output === "string" && outputs.output.trim()) {
+            return outputs.output;
+        }
+        const values = Object.entries(outputs)
+            .filter(([key, value]) => !key.toLowerCase().includes("reference") &&
+            typeof value === "string" &&
+            value.trim())
+            .map(([, value]) => value);
+        if (values.length)
+            return values.join("\n\n");
+    }
+    return streamedText;
+}
+export async function runCreateClinicalArticle(options) {
+    const format = options.format ?? "markdown";
+    const session = await requireClinicalSession(options.sessionId);
+    if (session.proofread?.outcome !== "success") {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "四要素尚未预检成功，无法生成全文");
+    }
+    if (isFourElementsDraftDrifted(session.precheckInputs, session.draft)) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_ARGUMENT, "四要素在预检后发生变化，请重新预检");
+    }
+    const appId = getClinicalFulltextAppId(session.researchObjective, session.topicInputs.Study_design);
+    const workflowInputs = {
+        ...fourElementsDraftToWorkflowInputs(session.draft),
+    };
+    if (session.topicInputs.Prognosis_model) {
+        workflowInputs.Prognosis_model =
+            session.topicInputs.Prognosis_model;
+    }
+    if (session.topicInputs.diagnostic_model) {
+        workflowInputs.diagnostic_model =
+            session.topicInputs.diagnostic_model;
+    }
+    process.stderr.write(`${CLINICAL_FULLTEXT_WAIT_HINT}\n`);
+    const stream = await streamClinicalWorkflow({
+        path: CLINICAL_EXECUTE_API_PATH,
+        body: buildClinicalWorkflowBody({
+            appId,
+            appName: `${session.researchObjective}-全文`,
+            appType: CLINICAL_WORKFLOW_APP_TYPE,
+            inputs: workflowInputs,
+        }),
+        format,
+        startLabel: "正在生成临床申请书全文...",
+        progressLabel: "全文生成中",
+        finishLabel: "全文生成完成",
+        failureMessage: "临床申请书全文生成失败，请稍后重试",
+        emptyMessage: "临床申请书全文结果为空",
+        allowEmptyText: true,
+    });
+    const rawArticle = pickClinicalFulltext(stream.outputs, stream.text).trim();
+    if (!rawArticle) {
+        throw new helixlifeError(helixlifeErrorCode.INVALID_RESPONSE, "临床申请书全文结果为空，请稍后重试");
+    }
+    const article = preprocessClinicalMarkdown(rawArticle).trim();
+    const references = extractReferences(stream.outputs);
+    const cacheReady = await updateClinicalSession(session, {
+        article: {
+            article,
+            references,
+            workflowRunId: stream.workflowRunId,
+        },
+    }).then(() => true);
+    const result = {
+        status: "article_ready",
+        nextAction: "download_article",
+        article,
+        references,
+    };
+    if (format === "json") {
+        printOutput(wrapWorkbenchResult(result, { step: "article", subType: "clinical" }, {
+            sessionId: session.sessionId,
+            workflowRunId: stream.workflowRunId,
+            cacheReady,
+        }), "json");
+        return;
+    }
+    const log = createFormatLogger(format);
+    log(`\n${article}\n`);
+    if (references.length) {
+        log(`\n## 参考文献\n\n${references.join("\n")}\n`);
+    }
+    log("\n全文已生成，可继续导出原始引文格式 MD 和 Word。\n");
+}
+//# sourceMappingURL=article-create.js.map

package/cli/dist/modules/fund/clinical/commands/article-create.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/clinical/commands/article-download.d.ts

@@ -0,0 +1,30 @@
+import { type OutputFormat } from "../../../../core/index.js";
+export interface DownloadClinicalArticleOptions {
+    sessionId?: string;
+    file?: string;
+    referencesFile?: string;
+    output?: string;
+    produceId?: string;
+    format?: OutputFormat;
+}
+export interface ClinicalArticleDownloadResult {
+    mdPath: string;
+    mdSize: number;
+    docxPath: string;
+    docxSize: number;
+    contentType: string | null;
+    filename: string;
+}
+/** 对齐网页标题语义：项目名称/标题/Title 优先，否则首个有效 H1。 */
+export declare function extractClinicalArticleTitle(markdown: string): string;
+export declare function appendClinicalReferences(article: string, references: string[]): string;
+export declare function resolveClinicalDownloadPaths(output: string | undefined, title: string): {
+    docxPath: string;
+    mdPath: string;
+};
+export declare function downloadClinicalArticleDocx(markdown: string, produceId: string): Promise<{
+    buffer: Buffer;
+    contentType: string | null;
+}>;
+export declare function runDownloadClinicalArticle(options: DownloadClinicalArticleOptions): Promise<ClinicalArticleDownloadResult>;
+//# sourceMappingURL=article-download.d.ts.map

package/cli/dist/modules/fund/clinical/commands/article-download.d.ts.map

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