helixlife-expert-cli 0.1.0

package/cli/dist/modules/fund/nsfc/index.js

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+import { parseOutputFormat } from "../../../core/index.js";
+import { runCreateNsfcHypothesis } from "./commands/hypothesis-create.js";
+import { runAnalyzeNsfcHypothesis } from "./commands/hypothesis-analyze.js";
+import { runNsfcGenesSelect } from "./commands/hypothesis-genes-select.js";
+import { runNsfcHypothesisPick } from "./commands/hypothesis-pick.js";
+import { runNsfcResearchPathConfirm } from "./commands/research-path-confirm.js";
+import { runCreateNsfcOutline } from "./commands/outline-create.js";
+import { runConfirmNsfcOutline } from "./commands/outline-confirm.js";
+import { runCreateNsfcArticle } from "./commands/article-create.js";
+import { runDownloadNsfcArticle } from "./commands/article-download.js";
+import { runNsfcTechRoadmap } from "./commands/tech-roadmap.js";
+import { runNsfcHypothesisFigure } from "./commands/hypothesis-figure.js";
+import { runNsfcFormatConvert } from "./commands/format-convert.js";
+/** 注册基金工作台（nsfc）子命令 */
+export function registerNsfcCommands(nsfc) {
+    const hypothesis = nsfc
+        .command("hypothesis")
+        .description("科学假说（Step1 采集 / Step2 确认）");
+    hypothesis
+        .command("create")
+        .description("Step1：选择是否有假说 → 填选项/文本/材料 → 校验通过后输出可串联参数（不调工作流）")
+        .option("--has-hypothesis <type>", "是否有科学假说：blank（无）| existing（有）")
+        .option("--project-level <level>", "项目级别：国家级 | 省部级")
+        .option("--project <type>", "项目类型（国家级必填）：面上项目 | 地区项目 | 青年项目")
+        .option("--prior-result <yes|no>", "是否有前期研究结果（仅 blank）：yes | no")
+        .option("-q, --query <text>", "主文本：blank 为疾病名/研究主题；existing 为科学假说；长文本请用 --query-file")
+        .option("--query-file <path>", "主文本文件路径（UTF-8，与 --query 互斥）")
+        .option("--disease <text>", "疾病名称（existing 必填；blank+有前期时通常与 --query 相同）")
+        .option("--disease-file <path>", "疾病名称文件路径（与 --disease 互斥）")
+        .option("--attach <path>", "补充材料本地路径（pdf/docx；blank+有前期必填，existing 可选）")
+        .option("-y, --yes", "跳过交互，直接使用参数（须提供全部当前路径必填项）")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runCreateNsfcHypothesis({
+            hasHypothesis: opts.hasHypothesis,
+            projectLevel: opts.projectLevel,
+            project: opts.project,
+            priorResult: opts.priorResult,
+            query: opts.query,
+            queryFile: opts.queryFile,
+            disease: opts.disease,
+            diseaseFile: opts.diseaseFile,
+            attach: opts.attach,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    hypothesis
+        .command("analyze")
+        .description("Step2①：按 Step1 nextSubStep 跑首个分析工作流（背景基因 / 假说列表 / 研究路径）")
+        .requiredOption("--has-hypothesis <type>", "blank | existing（Step1 _handoff）")
+        .requiredOption("--next-sub-step <step>", "background_genes | hypothesis_pick | research_path")
+        .requiredOption("--inputs-file <path>", "Step1 data.inputs JSON 文件路径")
+        .option("-q, --query <text>", "主文本（可省略，默认取 inputs.input/text）")
+        .option("--query-file <path>", "主文本文件（与 --query 互斥）")
+        .option("-y, --yes", "非交互（本命令无额外选型）")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runAnalyzeNsfcHypothesis({
+            hasHypothesis: opts.hasHypothesis,
+            nextSubStep: opts.nextSubStep,
+            inputsFile: opts.inputsFile,
+            query: opts.query,
+            queryFile: opts.queryFile,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const genes = hypothesis.command("genes").description("候选基因（有前期路径）");
+    genes
+        .command("select")
+        .description("提交候选基因 N 选 1，生成假说列表")
+        .requiredOption("--order-id <id>", "hypothesis analyze 返回的 orderId")
+        .option("--gene <name>", "候选基因名")
+        .option("--mechanism <text>", "机制/方向文案")
+        .option("--results <text>", "前期结果 pre_result")
+        .option("-y, --yes", "跳过交互，须提供 --gene / --mechanism")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcGenesSelect({
+            orderId: opts.orderId,
+            gene: opts.gene,
+            mechanism: opts.mechanism,
+            results: opts.results,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    hypothesis
+        .command("pick")
+        .description("Step2：确认科学假说（可选自定义）；仅输出 handoff，不跑提纲")
+        .requiredOption("--order-id <id>", "analyze 或 genes select 返回的 orderId")
+        .option("--hypothesis-index <n>", "假说列表下标（从 0 起）")
+        .option("--custom <text>", "自定义假说文本")
+        .option("--custom-file <path>", "自定义假说文件（与 --custom 互斥）")
+        .option("-y, --yes", "跳过交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcHypothesisPick({
+            orderId: opts.orderId,
+            hypothesisIndex: opts.hypothesisIndex,
+            custom: opts.custom,
+            customFile: opts.customFile,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const researchPath = nsfc
+        .command("research-path")
+        .description("已有假说：研究路径 + 缺失信息");
+    researchPath
+        .command("confirm")
+        .description("确认缺失信息并直接生成提纲（跳过补假说）")
+        .requiredOption("--order-id <id>", "hypothesis analyze 返回的 orderId")
+        .option("--picks-file <path>", "缺失信息选型 JSON：[{title,value},...]（有缺失信息时必填）")
+        .option("-y, --yes", "跳过交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcResearchPathConfirm({
+            orderId: opts.orderId,
+            picksFile: opts.picksFile,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const outline = nsfc.command("outline").description("申请书提纲（Step3）");
+    outline
+        .command("create")
+        .description("生成 / 重新生成提纲（读 Step2 会话假说与 outlineParams）")
+        .requiredOption("--order-id <id>", "Step2 返回的 orderId")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runCreateNsfcOutline({
+            orderId: opts.orderId,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    outline
+        .command("confirm")
+        .description("确认提纲（可选 --file 回传 Agent 本地修改后的 Markdown）")
+        .requiredOption("--order-id <id>", "会话 orderId")
+        .option("-f, --file <path>", "改稿后的提纲 Markdown 文件；缺省使用缓存中的提纲")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runConfirmNsfcOutline({
+            orderId: opts.orderId,
+            file: opts.file,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const article = nsfc.command("article").description("申请书全文（Step4）");
+    article
+        .command("create")
+        .description("基于已确认提纲生成申请书全文（SSE）")
+        .requiredOption("--order-id <id>", "会话 orderId")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runCreateNsfcArticle({
+            orderId: opts.orderId,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    article
+        .command("download")
+        .description("导出原始引文格式 Markdown + Word")
+        .option("--order-id <id>", "会话 orderId（命中全文缓存）")
+        .option("--file <path>", "本地 Markdown 全文（与 --order-id 互斥）")
+        .option("-o, --output <path>", "输出 .docx 路径或目录")
+        .option("--produce-id <id>", "AIGC produce_id（默认取 workflowRunId）")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runDownloadNsfcArticle({
+            orderId: opts.orderId,
+            file: opts.file,
+            output: opts.output,
+            produceId: opts.produceId,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const techRoadmap = nsfc
+        .command("tech-roadmap")
+        .description("技术路线图（基于提纲立项依据，只出图）");
+    techRoadmap
+        .command("create")
+        .description("生成技术路线图 Mermaid/PNG（不插入全文）")
+        .requiredOption("--order-id <id>", "会话 orderId")
+        .option("-o, --output <dir>", "图片输出目录（默认 Downloads/nsfc-tech-roadmap）")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcTechRoadmap({
+            orderId: opts.orderId,
+            output: opts.output,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    const hypothesisFigure = nsfc
+        .command("hypothesis-figure")
+        .description("假说机制图（基于科学假说，只出图）");
+    hypothesisFigure
+        .command("create")
+        .description("生成假说机制图 PNG（不插入全文）")
+        .requiredOption("--order-id <id>", "会话 orderId")
+        .option("-o, --output <dir>", "图片输出目录（默认 Downloads）")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcHypothesisFigure({
+            orderId: opts.orderId,
+            output: opts.output,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+    nsfc
+        .command("format-convert")
+        .description("格式转换：全文 Markdown → 改写 → Word（全项目类型）")
+        .requiredOption("--order-id <id>", "会话 orderId")
+        .option("-o, --output <path>", "输出 .docx 路径或目录")
+        .option("-y, --yes", "非交互")
+        .option("--format <format>", "输出格式：markdown | json", "markdown")
+        .action(async (opts) => {
+        await runNsfcFormatConvert({
+            orderId: opts.orderId,
+            output: opts.output,
+            yes: opts.yes,
+            format: parseOutputFormat(opts.format),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/cli/dist/modules/fund/nsfc/index.js.map

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package/cli/dist/modules/fund/nsfc/mermaid-render.d.ts

@@ -0,0 +1,18 @@
+export interface MermaidRenderResult {
+    mmdPath: string;
+    pngPath?: string;
+    rendered: boolean;
+    method?: "graph-layout";
+    error?: string;
+}
+export interface RenderMermaidOptions {
+    /** 横向排布（对齐原站：动物/临床水平用横排，细胞用纵排） */
+    horizontal?: boolean;
+}
+/**
+ * 去掉 Markdown 代码围栏（对齐原站 tech-roadmap-modal）
+ * 工作流常返回 ```mermaid ... ```，需纯 Mermaid 源码。
+ */
+export declare function stripMermaidFences(source: string): string;
+export declare function renderMermaidToPng(mermaidSource: string, outputBasePath: string, options?: RenderMermaidOptions): Promise<MermaidRenderResult>;
+//# sourceMappingURL=mermaid-render.d.ts.map

package/cli/dist/modules/fund/nsfc/mermaid-render.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"mermaid-render.d.ts","sourceRoot":"","sources":["../../../../src/modules/fund/nsfc/mermaid-render.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,mBAAmB;IAClC,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,oBAAoB;IACnC,kCAAkC;IAClC,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAOzD;AAED,wBAAsB,kBAAkB,CACtC,aAAa,EAAE,MAAM,EACrB,cAAc,EAAE,MAAM,EACtB,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,mBAAmB,CAAC,CA0B9B"}

package/cli/dist/modules/fund/nsfc/mermaid-render.js

@@ -0,0 +1,47 @@
+/**
+ * Mermaid → PNG：graph-layout（服务端布局，与原站同源）+ Resvg。
+ * 与工作流同前提：网络 + token；不依赖本机 Chrome / mmdc。
+ */
+import { writeFile } from "node:fs/promises";
+import { renderMermaidViaGraphLayout } from "./graph-render.js";
+/**
+ * 去掉 Markdown 代码围栏（对齐原站 tech-roadmap-modal）
+ * 工作流常返回 ```mermaid ... ```，需纯 Mermaid 源码。
+ */
+export function stripMermaidFences(source) {
+    let s = source.trim();
+    const fenced = /^```(?:mermaid)?\s*\r?\n?([\s\S]*?)\r?\n?```\s*$/i;
+    const matched = s.match(fenced);
+    if (matched)
+        return matched[1].trim();
+    s = s.replace(/^```(?:mermaid)?\s*\r?\n?/i, "").replace(/\r?\n?```\s*$/i, "");
+    return s.trim();
+}
+export async function renderMermaidToPng(mermaidSource, outputBasePath, options = {}) {
+    const mmdPath = `${outputBasePath}.mmd`;
+    const pngPath = `${outputBasePath}.png`;
+    const clean = stripMermaidFences(mermaidSource);
+    if (!clean) {
+        await writeFile(mmdPath, "\n", "utf8");
+        return {
+            mmdPath,
+            rendered: false,
+            error: `Mermaid 源码为空（已跳过渲染）：${outputBasePath}`,
+        };
+    }
+    await writeFile(mmdPath, clean + "\n", "utf8");
+    try {
+        const png = await renderMermaidViaGraphLayout(clean, options.horizontal);
+        await writeFile(pngPath, png);
+        return { mmdPath, pngPath, rendered: true, method: "graph-layout" };
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        return {
+            mmdPath,
+            rendered: false,
+            error: `Mermaid PNG 渲染失败（已保存 ${mmdPath}）：${message.slice(0, 300)}`,
+        };
+    }
+}
+//# sourceMappingURL=mermaid-render.js.map

package/cli/dist/modules/fund/nsfc/mermaid-render.js.map

@@ -0,0 +1 @@
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package/cli/dist/modules/fund/nsfc/parse-hypothesis.d.ts

@@ -0,0 +1,76 @@
+export interface NsfcHypothesisItem {
+    id: string;
+    original_text: string;
+    new_text: string;
+    background_report?: string;
+    mechanism?: string;
+    results?: string;
+    gene?: string;
+    directions?: string[];
+}
+export interface NsfcMissingInfoBlock {
+    title: string;
+    select: string[];
+}
+/** WorkBuddy / AskQuestion 可直接使用的候选基因选项 */
+export interface NsfcGeneSelectionOption {
+    index: number;
+    label: string;
+    description: string;
+    value: string;
+    mechanism: string;
+    results: string;
+}
+/** WorkBuddy / AskQuestion 可直接使用的假说选项（含自定义） */
+export interface NsfcHypothesisSelectionOption {
+    index: number;
+    label: string;
+    description: string;
+    value: string;
+}
+/** 缺失信息单块内的选择器选项（label=短标题；全文在 description / value） */
+export interface NsfcMissingInfoSelectionOption {
+    index: number;
+    label: string;
+    description: string;
+    value: string;
+}
+/** 拼接候选基因的研究方向文案（directions 全量；无则 mechanism） */
+export declare function formatGeneResearchDirections(g: NsfcHypothesisItem): string;
+/**
+ * 缺失信息选项短标题：取括号前机制名（如 `ceRNA机制 (…)` → `ceRNA机制`）；
+ * 无括号则用全文。对齐「聊天展示全文 + 选择器短标题」。
+ */
+export declare function shortMissingInfoLabel(full: string): string;
+/**
+ * 构造候选基因选择器选项。
+ * UX：聊天先按基因列出研究方向全文；选择器 label 仅基因名（勿重复塞进 label）。
+ */
+export declare function buildGeneSelectionOptions(genes: NsfcHypothesisItem[]): NsfcGeneSelectionOption[];
+/**
+ * 构造假说选择器选项。
+ * UX：聊天完整展示假说正文；选择器仅短标题（假说 N）。
+ */
+export declare function buildHypothesisSelectionOptions(hypotheses: NsfcHypothesisItem[]): NsfcHypothesisSelectionOption[];
+/**
+ * 构造缺失信息单块选择器选项。
+ * UX：聊天先列出选项全文（含括号说明）；选择器 label 仅短标题；
+ * value 仍为工作流全文，供 --picks-file 提交。
+ */
+export declare function buildMissingInfoBlockSelectionOptions(block: NsfcMissingInfoBlock): NsfcMissingInfoSelectionOption[];
+export declare function articleContentToJsonArrayString(raw: string): string;
+export declare function splitGeneDirectionLines(direction: string): string[];
+/** 解析假说列表 outputs.jsonN */
+export declare function parseNsfcV2HypothesisWorkflowResult(outputs: unknown): NsfcHypothesisItem[] | null;
+/** 解析文章分析 outputs.result → 背景 + 候选基因 */
+export declare function parseNsfcV2ArticleWorkflowResult(result: unknown): {
+    backgroundReport: string;
+    genes: NsfcHypothesisItem[];
+} | null;
+export declare function buildNsfcV2GenePreResultsText(genes: NsfcHypothesisItem[] | null | undefined): string;
+export declare function getResearchPathReportText(result: unknown): string;
+export declare function parseMissingInfoFromAnalysisResult(result: unknown): NsfcMissingInfoBlock[];
+export declare function isMissingInfoCustomOption(optionLabel: string): boolean;
+/** 从 outputs 统一尝试解析假说列表 */
+export declare function tryParseHypothesisList(outputs: Record<string, unknown> | undefined): NsfcHypothesisItem[];
+//# sourceMappingURL=parse-hypothesis.d.ts.map

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